Mercurial > repos > bgruening > diffbind
annotate diffbind.xml @ 30:6b235ac52faf draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
| author | iuc |
|---|---|
| date | Mon, 08 Jul 2024 18:31:37 +0000 |
| parents | 3aa2c26cc990 |
| children |
| rev | line source |
|---|---|
|
30
6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
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1 <tool id="diffbind" name="DiffBind" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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22
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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2 <description> differential binding analysis of ChIP-Seq peak data</description> |
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30
6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
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3 <macros> |
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6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
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4 <token name="@TOOL_VERSION@">3.12.0</token> |
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6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
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5 <token name="@VERSION_SUFFIX@">0</token> |
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6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
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6 <token name="@PROFILE@">22.05</token> |
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6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
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7 </macros> |
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29
3aa2c26cc990
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
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diff
changeset
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8 <xrefs> |
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3aa2c26cc990
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
28
diff
changeset
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9 <xref type="bio.tools">diffbind</xref> |
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30
6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
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10 <xref type="bioconductor">diffbind</xref> |
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29
3aa2c26cc990
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
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diff
changeset
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11 </xrefs> |
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22
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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12 <requirements> |
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30
6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
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13 <requirement type="package" version="@TOOL_VERSION@">bioconductor-diffbind</requirement> |
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6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
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14 <requirement type="package" version="1.20.4">r-getopt</requirement> |
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6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
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15 <requirement type="package" version="4.0.16">bioconductor-edger</requirement> |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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16 </requirements> |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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17 <stdio> |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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18 <regex match="Execution halted" |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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19 source="both" |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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20 level="fatal" |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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21 description="Execution halted." /> |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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22 <regex match="Input-Error 01" |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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23 source="both" |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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24 level="fatal" |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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25 description="Error in your input parameters: Make sure you only apply factors to selected samples." /> |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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26 <regex match="Error in" |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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27 source="both" |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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28 level="fatal" |
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24
15bbd86c6c7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
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diff
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29 description="An undefined error occured, please check your input carefully and contact your administrator." /> |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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30 </stdio> |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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31 <version_command><![CDATA[ |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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32 echo $(R --version | grep version | grep -v GNU)", DiffBind version" $(R --vanilla --slave -e "library(DiffBind); cat(sessionInfo()\$otherPkgs\$DiffBind\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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33 ]]></version_command> |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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34 <command><![CDATA[ |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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35 #import re |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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changeset
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36 #import json |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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changeset
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37 |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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changeset
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38 ## Adapted from DESeq2 wrapper |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
22
diff
changeset
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39 #set $temp_factor_names = list() |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
22
diff
changeset
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40 #set $temp_factor = list() |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
22
diff
changeset
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41 |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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diff
changeset
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42 #for $g in $rep_group: |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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43 |
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30
6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
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44 #set $peak_files = dict() |
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6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
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45 #set $bam_files = dict() |
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6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
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46 #set $bam_controls = dict() |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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47 |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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48 #for $file in $g.peaks: |
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405e17318279
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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49 #set $file_name = str($g.groupName) + "-" + re.sub('[^\w\-]', '_', str($file.element_identifier)) + "-peaks.bed" |
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405e17318279
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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50 ln -s '${file}' '${file_name}' && |
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30
6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
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51 #set $peak_files[str($file.element_identifier)] = str($file_name) |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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52 #end for |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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53 |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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54 #for $bam in $g.bamreads: |
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405e17318279
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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diff
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55 #set $bam_name = re.sub('[^\w\-]', '_', str($bam.element_identifier)) |
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405e17318279
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
25
diff
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56 #set $bam_file = $bam_name + "-bamreads.bam" |
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405e17318279
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
25
diff
changeset
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57 #set $bam_index = $bam_name + "-bamreads.bai" |
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405e17318279
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
25
diff
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58 ln -s '${bam}' '${bam_file}' && |
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405e17318279
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
25
diff
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59 ln -s '${bam.metadata.bam_index}' '${bam_index}' && |
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6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
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60 #set $bam_files[str($bam.element_identifier)] = str($bam_file) |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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61 #end for |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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62 |
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30
6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
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63 #if len($peak_files.keys()) != len($bam_files.keys()) |
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6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
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64 >&2 echo "Group $g.groupName: same number of Peak and Bam files needs to be given" && exit 1 && |
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6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
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65 #end if |
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6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
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66 $temp_factor.append( {str($g.groupName): [f[1] for f in sorted($peak_files.items())]} ) |
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6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
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67 $temp_factor.append( {str($g.groupName): [f[1] for f in sorted($bam_files.items())]} ) |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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68 |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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69 #if str( $g.bamcontrol ) != 'None': |
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393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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70 #for $ctrl in $g.bamcontrol: |
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405e17318279
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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71 #set $ctrl_name = re.sub('[^\w\-]', '_', str($ctrl.element_identifier)) |
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405e17318279
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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72 #set $ctrl_file = $ctrl_name + "-bamcontrol.bam" |
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6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
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73 #set $ctrl_index = $ctrl_name + "-bamcontrol.bai" |
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405e17318279
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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74 #if $ctrl_file not in json.dumps($temp_factor): |
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405e17318279
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
25
diff
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75 ln -s '${ctrl}' '${ctrl_file}' && |
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405e17318279
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
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76 ln -s '${ctrl.metadata.bam_index}' '${ctrl_index}' && |
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77 #end if |
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78 #set $bam_controls[str($ctrl.element_identifier)] = str($ctrl_file) |
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79 #end for |
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80 #if len($peak_files.keys()) != len($bam_files.keys()) |
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81 >&2 echo "Group $g.groupName: same number of Peak and Bam control files needs to be given" && exit 1 && |
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82 #end if |
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83 $temp_factor.append( {str($g.groupName): [f[1] for f in sorted($bam_controls.items())]} ) |
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84 #end if |
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85 |
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86 #end for |
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87 |
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88 $temp_factor.reverse() |
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89 $temp_factor_names.append(["Condition", $temp_factor]) |
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90 |
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91 |
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92 Rscript '$__tool_directory__/diffbind.R' |
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93 |
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94 -i '#echo json.dumps(temp_factor_names)#' |
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95 -o '$outfile' |
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96 -m '$method' |
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97 -t $th |
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98 -f $out.format |
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99 -p '$plots' |
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100 -O $minoverlap |
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101 #if $use_blacklist: |
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102 -B |
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103 #end if |
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104 -n $scorecol |
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105 #if $lowerbetter: |
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106 -l "$lowerbetter" |
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107 #end if |
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108 #if $summits: |
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109 -s "$summits" |
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110 #end if |
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111 |
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112 #if $out.binding_matrix: |
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113 -b |
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114 #end if |
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115 |
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116 #if $out.rdata: |
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117 -r |
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118 #end if |
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119 |
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120 #if $out.analysis_info: |
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121 -a |
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122 #end if |
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123 |
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124 #if $out.rscript: |
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125 && cp '$__tool_directory__/diffbind.R' '$rscript' |
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126 #end if |
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127 ]]> |
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128 </command> |
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129 <inputs> |
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130 <repeat name="rep_group" title="Group" min="2" max="2" default="2"> |
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131 <param name="groupName" type="text" label="Name" |
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132 help="Name for the Group that the peak and BAM files belong to e.g. Resistant/Responsive (two Groups must be specified for DiffBind). NOTE: Please only use letters, numbers or underscores."> |
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133 <sanitizer> |
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134 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
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135 </sanitizer> |
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136 <validator type="empty_field" /> |
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137 </param> |
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138 <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/> |
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139 <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM files" help="Specify the Read BAM files used in the Peak calling. The input order of the BAM files for the samples MUST match the input order of the peaks files."/> |
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140 <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM files" help="If specifying a control BAM file, all samples are required to specify one, see Help section below. The input order of the BAM files for the samples MUST match the input order of the peaks files."/> |
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141 </repeat> |
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142 <param name="method" type="select" label="Underlying method by which to analyze differential binding affinity"> |
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143 <option value="DBA_DESEQ2" selected="True">DESeq2</option> |
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144 <option value="DBA_EDGER">edgeR</option> |
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145 </param> |
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146 <param name="use_blacklist" type="boolean" truevalue="True" falsevalue="" checked="False" label="Filters peak intervals that overlap a blacklist from ENCODE" help="Works with human, mouse, worm and fly. Assembly version is determined from the BAM files." /> |
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147 <param name="minoverlap" type="integer" min="1" value="2" label="Only include peaks in at least this many peaksets in the main binding matrix"> |
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148 <sanitizer> |
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149 <valid initial="string.digits"/> |
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150 </sanitizer> |
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151 </param> |
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152 <param name="scorecol" type="integer" min="0" value="5" label="Score Column" help="Column in peak files that contains peak scores. Default: 5 (narrowPeak)"> |
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153 <sanitizer> |
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154 <valid initial="string.digits"/> |
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155 </sanitizer> |
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156 </param> |
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157 <param name="lowerbetter" type="boolean" truevalue="True" falsevalue="" checked="False" label="Lower score is better?" help="DiffBind by default assumes that a higher score indicates a better peak, for example narrowPeaks -log10pvalue. If this is not the case, for example if the score is a p-value or FDR, set this option to Yes. Default: No" /> |
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158 <param name="summits" type="integer" min="0" optional="True" label="Summits" help="Extend peaks Nbp up- and downstream of the summit. For punctate peaks it is advisable to extend (e.g. 250bp), see the DiffBind User Guide"> |
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159 <sanitizer> |
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160 <valid initial="string.digits"/> |
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161 </sanitizer> |
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162 </param> |
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163 <param name="th" type="float" value="0.05" min="0" max="1" label="FDR Threshold" help="Significance threshold; all sites with FDR less than or equal to this value will be included in the output. A value of 1 will output all binding sites. Default: 0.05"/> |
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164 |
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165 <!-- Output Options --> |
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166 <section name="out" expanded="false" title="Output Options"> |
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167 <param name="format" type="select" label="Output Format"> |
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168 <option value="interval" selected="True">Interval</option> |
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169 <option value="bed">BED</option> |
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170 <option value="tabular">Tabular (tab-separated)</option> |
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171 </param> |
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172 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="False" label="Visualising the analysis results" help="output an additional PDF file" /> |
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173 <param name="binding_matrix" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output binding affinity matrix?" help="Output a table of the binding scores" /> |
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174 <param name="rdata" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output RData file?" help="Output all the data used by R to construct the plots and tables, can be loaded into R. Default: No"/> |
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175 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/> |
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176 <param name="analysis_info" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output analysis info?" help="If this option is set to Yes, information from the dba.count and dba.analyze commmands will be output in a text file. Default: No"/> |
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177 </section> |
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178 </inputs> |
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179 |
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180 <outputs> |
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181 <data name="outfile" format="interval" label="${tool.name} on ${on_string}: Differentially bound sites"> |
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182 <change_format> |
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183 <when input="out.format" value="bed" format="bed" /> |
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184 <when input="out.format" value="tabular" format="tabular" /> |
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185 </change_format> |
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186 </data> |
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187 <data name="plots" format="pdf" label="${tool.name} on ${on_string}: Plots"> |
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188 <filter>out['pdf']</filter> |
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189 </data> |
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190 <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="${tool.name} on ${on_string}: Binding matrix"> |
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191 <filter>out['binding_matrix']</filter> |
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192 </data> |
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193 <data name="rdata" format="rdata" from_work_dir="DiffBind_analysis.RData" label="${tool.name} on ${on_string}: RData file"> |
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194 <filter>out['rdata']</filter> |
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195 </data> |
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196 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript"> |
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197 <filter>out['rscript']</filter> |
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198 </data> |
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199 <data name="analysis_info" format="txt" from_work_dir="DiffBind_analysis_info.txt" label="${tool.name} on ${on_string}: Analysis info"> |
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200 <filter>out['analysis_info']</filter> |
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201 </data> |
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202 </outputs> |
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203 |
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204 <tests> |
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205 <!-- Ensure outputs work --> |
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206 <test expect_num_outputs="6"> |
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207 <repeat name="rep_group"> |
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208 <param name="groupName" value="Resistant"/> |
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209 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
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210 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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211 </repeat> |
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212 <repeat name="rep_group"> |
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213 <param name="groupName" value="Responsive"/> |
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214 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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215 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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216 </repeat> |
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217 <param name="scorecol" value="5" /> |
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218 <param name="format" value="interval"/> |
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219 <param name="pdf" value="True" /> |
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220 <param name="binding_matrix" value="True" /> |
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221 <param name="rdata" value="True" /> |
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222 <param name="rscript" value="True"/> |
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223 <param name="analysis_info" value="True"/> |
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224 <output name="outfile" ftype="interval" value="out_diffbind.interval" /> |
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225 <output name="plots" value="out_plots.pdf" compare="sim_size" /> |
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226 <output name="binding_matrix" value="out_binding_matrix.tab" /> |
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23
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227 <output name="rdata" value="DiffBind_analysis.RData" compare="sim_size"/> |
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25
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228 <output name="rscript"> |
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229 <assert_contents> |
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230 <has_text text="write.table"/> |
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231 </assert_contents> |
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232 </output> |
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233 <output name="analysis_info" compare="sim_size" > |
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23
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234 <assert_contents> |
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235 <has_text text="SessionInfo"/> |
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236 </assert_contents> |
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237 </output> |
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22
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238 </test> |
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30
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239 <!-- Ensure EDGER works --> |
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240 <test expect_num_outputs="3"> |
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241 <repeat name="rep_group"> |
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242 <param name="groupName" value="Resistant"/> |
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243 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
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244 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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245 </repeat> |
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246 <repeat name="rep_group"> |
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247 <param name="groupName" value="Responsive"/> |
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248 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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249 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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250 </repeat> |
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251 <param name="scorecol" value="5" /> |
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252 <param name="method" value="DBA_EDGER" /> |
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253 <param name="format" value="interval"/> |
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254 <param name="pdf" value="True" /> |
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255 <param name="binding_matrix" value="True" /> |
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256 <param name="rscript" value="False"/> |
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257 <output name="outfile" ftype="interval" value="out_diffbind_edger.interval" /> |
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258 <output name="plots" value="out_plots_edger.pdf" compare="sim_size" /> |
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259 <output name="binding_matrix" value="out_binding_matrix_edger.tab" /> |
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260 </test> |
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26
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261 <!-- Ensure control BAMs input works --> |
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262 <test expect_num_outputs="1"> |
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263 <repeat name="rep_group"> |
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264 <param name="groupName" value="Resistant"/> |
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265 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
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405e17318279
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266 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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267 <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" /> |
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268 </repeat> |
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269 <repeat name="rep_group"> |
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270 <param name="groupName" value="Responsive"/> |
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271 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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272 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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405e17318279
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273 <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" /> |
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274 </repeat> |
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275 <param name="scorecol" value="5" /> |
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276 <param name="format" value="interval"/> |
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277 <output name="outfile" ftype="interval" value="out_diffbind_ctrl.interval" /> |
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278 </test> |
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25
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279 <!-- Ensure BED output works --> |
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280 <test expect_num_outputs="1"> |
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281 <repeat name="rep_group"> |
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282 <param name="groupName" value="Resistant"/> |
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283 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
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09aabce86f5a
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284 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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285 </repeat> |
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286 <repeat name="rep_group"> |
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287 <param name="groupName" value="Responsive"/> |
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288 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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289 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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290 </repeat> |
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291 <param name="scorecol" value="5" /> |
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292 <param name="format" value="bed"/> |
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293 <output name="outfile" ftype="bed" value="out_diffbind.bed" /> |
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294 </test> |
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295 <!-- Ensure tabular output works --> |
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296 <test expect_num_outputs="1"> |
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297 <repeat name="rep_group"> |
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09aabce86f5a
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298 <param name="groupName" value="Resistant"/> |
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299 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
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09aabce86f5a
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300 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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301 </repeat> |
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302 <repeat name="rep_group"> |
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303 <param name="groupName" value="Responsive"/> |
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304 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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305 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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306 </repeat> |
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307 <param name="scorecol" value="5" /> |
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308 <param name="format" value="tabular"/> |
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309 <output name="outfile" ftype="tabular" file="out_diffbind.tab" /> |
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310 </test> |
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311 <!-- Ensure minoverlap works --> |
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312 <test expect_num_outputs="1"> |
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313 <repeat name="rep_group"> |
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314 <param name="groupName" value="Resistant"/> |
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315 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
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316 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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317 </repeat> |
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318 <repeat name="rep_group"> |
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319 <param name="groupName" value="Responsive"/> |
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320 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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321 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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322 </repeat> |
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323 <param name="minoverlap" value="1" /> |
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324 <param name="scorecol" value="5" /> |
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325 <param name="format" value="tabular"/> |
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326 <output name="outfile" ftype="tabular" file="out_diffbind_minoverlap1.tab" /> |
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327 </test> |
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328 <!-- Ensure blacklist filtering works --> |
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329 <test expect_num_outputs="1"> |
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330 <repeat name="rep_group"> |
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331 <param name="groupName" value="Resistant"/> |
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332 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
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333 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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334 </repeat> |
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335 <repeat name="rep_group"> |
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336 <param name="groupName" value="Responsive"/> |
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337 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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338 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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339 </repeat> |
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340 <param name="use_blacklist" value="True"/> |
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341 <param name="scorecol" value="5" /> |
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342 <param name="format" value="tabular"/> |
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343 <output name="outfile" ftype="tabular" file="out_diffbind_blacklist.tab" /> |
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344 </test> |
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345 </tests> |
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346 <help><![CDATA[ |
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347 |
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348 .. class:: infomark |
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349 |
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350 **What it does** |
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351 |
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352 DiffBind_ is a `Bioconductor package`_ that provides functions for processing ChIP-Seq data enriched for genomic loci where specific |
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353 protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and |
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354 aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously, |
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355 representing different ChIP experiments (antibodies, transcription factor and/or histone |
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356 marks, experimental conditions, replicates) as well as managing the results of multiple peak |
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357 callers. |
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358 |
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359 The primary emphasis of DiffBind is on identifying sites that are differentially bound |
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360 between two sample groups. It includes functions to support the processing of peak sets, |
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361 including overlapping and merging peak sets, counting sequencing reads overlapping intervals |
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362 in peak sets, and identifying statistically significantly differentially bound sites based on |
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363 evidence of binding affinity (measured by differences in read densities). To this end it uses |
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364 statistical routines developed in an RNA-Seq context (primarily the Bioconductor packages |
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365 edgeR and DESeq2). Additionally, the package builds on Rgraphics routines to provide a |
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366 set of standardized plots to aid in binding analysis. |
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367 |
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368 The `DiffBind User Guide`_ includes a brief overview of the processing flow, followed by four sections of |
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369 examples: the first focusing on the core task of obtaining differentially bound sites based on |
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370 affinity data, the second working through the main plotting routines, the third discussing the |
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371 use of a blocking factor, and the fourth revisiting occupancy data (peak calls) in more detail, |
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372 as well as comparing the results of an occupancy-based analysis with an affinity-based one. |
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373 Finally, certain technical aspects of the how these analyses are accomplished are detailed. |
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374 |
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375 **Note this DiffBind tool requires a minimum of four samples (two groups with two replicates each).** |
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376 |
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377 ----- |
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378 |
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379 **Inputs** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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380 |
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381 DiffBind works primarily with peaksets, which are sets of genomic intervals representing |
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382 candidate protein binding sites. Each interval consists of a chromosome, a start and end |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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383 position, and usually a score of some type indicating confidence in, or strength of, the peak. |
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384 Associated with each peakset are metadata relating to the experiment from which the peakset |
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385 was derived. Additionally, files containing mapped sequencing reads (BAM files) need to |
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386 be associated with each peakset (one for the ChIP data, and optionally another representing |
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387 a control sample) |
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388 |
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389 Inputs for a group will be sorted by identifier before processing. For each group the corresponding |
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390 sets of peak and BAM files need to be provided. Ideally this is accomplished by providing the data in |
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391 collections. |
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392 |
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393 |
|
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394 **Groups** |
|
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395 |
|
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396 You have to specify the name of the Group and the peak and BAM files for the two Groups you want to compare (e.g Resistant and Responsive) in the tool form above. |
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397 |
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398 Example: |
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399 |
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400 ============= ============= |
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401 **Sample** **Group** |
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402 ------------- ------------- |
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403 BT4741 Resistant |
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404 BT4742 Resistant |
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405 MCF71 Responsive |
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406 MCF72 Responsive |
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407 ============= ============= |
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408 |
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409 |
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410 **Peak files** |
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411 |
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412 Result of your Peak calling experiment in bed format, one file for each sample is required. The peak caller, format and score column can be specified in the tool form above. The default settings expect narrowPeak bed format, which has the score in the 8th column (-log10pvalue), and can be output from MACS2. |
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413 |
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414 Example: |
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415 |
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416 ======= ======= ======= =============== ============== |
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417 1 2 3 4 **5 (Score)** |
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418 ======= ======= ======= =============== ============== |
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419 chr18 215562 216063 peak_16037 56.11 |
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420 chr18 311530 312105 peak_16038 222.49 |
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421 chr18 356656 357315 peak_16039 92.06 |
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422 chr18 371110 372092 peak_16040 123.86 |
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423 chr18 395116 396464 peak_16041 1545.39 |
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424 chr18 399014 400382 peak_16042 1835.19 |
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425 chr18 499134 500200 peak_16043 748.32 |
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426 chr18 503518 504552 peak_16044 818.30 |
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427 chr18 531672 532274 peak_16045 159.30 |
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428 chr18 568326 569282 peak_16046 601.11 |
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429 ======= ======= ======= =============== ============== |
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430 |
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431 * BAM file which contains the mapped sequencing reads associated with each peakset, one file for each sample is required. |
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432 * Optional: Control BAM file representing a control dataset. If used, has to be specified for all samples. Note that the DiffBind authors say control reads are best utilized prior to running DiffBind, at the peak calling stage (e.g. with MACS2) and in blacklists, see this `Bioconductor post`_. |
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433 |
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434 ----- |
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435 |
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436 **Outputs** |
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437 |
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438 This tool outputs |
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439 |
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25
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440 * a table of differentially bound sites in Interval, BED or Tabular 0-based format |
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441 |
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442 Optionally, under **Output Options** you can choose to output |
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443 |
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444 * a PDF of plots (Heatmap, PCA, MA, Volcano, Boxplots) |
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445 * a binding affinity matrix |
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446 * the R script used by this tool |
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447 * an RData file of the R objects generated |
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448 * a text file with information on the analysis (number of Intervals, FriP scores, method used) |
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449 |
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450 **Differentially Bound Sites** |
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451 |
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452 The default output is Interval format, for information on Interval format see here_. Alternatively, you can choose to output BED or Tabular 0-based format as below. For an explanation of the 0-based and 1-based coordinate systems see this `Biostars post`_. |
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453 |
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454 Example - **Interval format**: |
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455 |
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456 ====== ====== ====== ======== ===== ====== =========================================== |
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457 Chrom Start End Name Score Strand **Comment** |
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458 ====== ====== ====== ======== ===== ====== =========================================== |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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diff
changeset
|
459 chr18 394599 396513 DiffBind 0 \. 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
460 chr18 111566 112005 DiffBind 0 \. 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
461 chr18 346463 347342 DiffBind 0 \. 879|5|5.77|3.24|2.52|6.51e-06|0.00303 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
462 chr18 399013 400382 DiffBind 0 \. 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
463 chr18 371109 372102 DiffBind 0 \. 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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diff
changeset
|
464 ====== ====== ====== ======== ===== ====== =========================================== |
|
22
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
|
465 |
|
24
15bbd86c6c7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
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changeset
|
466 Columns contain the following data: |
|
22
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
|
467 |
|
25
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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diff
changeset
|
468 * **Chrom**: Chromosome name |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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changeset
|
469 * **Start**: Start position of site |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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diff
changeset
|
470 * **End**: End position of site |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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diff
changeset
|
471 * **Score**: 0 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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changeset
|
472 * **Name**: DiffBind |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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changeset
|
473 * **Strand**: Strand |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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changeset
|
474 * **Comment**: The pipe ("|") separated values in this column correspond to: |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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diff
changeset
|
475 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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diff
changeset
|
476 * *width*: Length of site |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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diff
changeset
|
477 * *Conc*: Mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted) |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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changeset
|
478 * *Conc_Group1*: Mean concentration over the first group (e.g. Responsive) |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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changeset
|
479 * *Conc_Group2*: Mean concentration over second group (e.g. Resistant) |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
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changeset
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480 * *Fold*: Fold shows the difference in mean concentrations between the two groups (e.g. Responsive - Resistant), with a positive value indicating increased binding affinity in the first group and a negative value indicating increased binding affinity in the second group. |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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diff
changeset
|
481 * *p.value*: P-value confidence measure for identifying these sites as differentially bound |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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changeset
|
482 * *FDR*: a multiple testing corrected FDR p-value |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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diff
changeset
|
483 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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changeset
|
484 Example - **BED format**: |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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diff
changeset
|
485 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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diff
changeset
|
486 ===== ====== ====== ======== ===== ====== |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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diff
changeset
|
487 Chrom Start End Name Score Strand |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
488 ===== ====== ====== ======== ===== ====== |
|
30
6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
|
489 chr18 394599 396513 DiffBind 0 \. |
|
6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
|
490 chr18 111566 112005 DiffBind 0 \. |
|
6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
|
491 chr18 346463 347342 DiffBind 0 \. |
|
6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
|
492 chr18 399013 400382 DiffBind 0 \. |
|
6b235ac52faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
29
diff
changeset
|
493 chr18 371109 372102 DiffBind 0 \. |
|
25
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
494 ===== ====== ====== ======== ===== ====== |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
495 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
496 Example - **Tabular format**: |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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diff
changeset
|
497 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
498 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ======== |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
499 Chrom Start End Name Score Strand Conc Conc_Responsive Conc_Resistant Fold p.value FDR |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
500 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ======== |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
501 chr18 394599 396513 DiffBind 0 \. 7.15 5.55 7.89 -2.35 7.06E-24 9.84E-21 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
502 chr18 111566 112005 DiffBind 0 \. 5.71 6.53 3.63 2.89 1.27E-08 8.88E-06 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
503 chr18 346463 347342 DiffBind 0 \. 5 5.77 3.24 2.52 6.51E-06 0.00303 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
504 chr18 399013 400382 DiffBind 0 \. 7.62 7 8.05 -1.04 1.04E-05 0.00364 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
505 chr18 371109 372102 DiffBind 0 \. 4.63 3.07 5.36 -2.3 8.10E-05 0.0226 |
|
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
506 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ======== |
|
22
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
|
507 |
|
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
|
508 |
|
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
|
509 **Binding Affinity Matrix** |
|
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
|
510 |
|
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
|
511 The final result of counting is a binding affinity matrix containing a (normalized) read count for each sample at every potential binding site. With this matrix, the samples can be re-clustered using affinity, rather than occupancy, data. The binding affinity matrix can be used for QC plotting as well as for subsequent |
|
25
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
24
diff
changeset
|
512 differential analysis. Note that this output is a tabular 0-based format. |
|
22
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
|
513 |
|
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
|
514 Example: |
|
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
|
515 |
|
24
15bbd86c6c7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
23
diff
changeset
|
516 ===== ====== ====== ========= ========= ========== ========== |
|
25
09aabce86f5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents:
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diff
changeset
|
517 Chrom Start End MCF7_ER_1 MCF7_ER_2 BT474_ER_1 BT474_ER_2 |
|
24
15bbd86c6c7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
23
diff
changeset
|
518 ===== ====== ====== ========= ========= ========== ========== |
|
15bbd86c6c7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
23
diff
changeset
|
519 chr18 111567 112005 137.6152 59.87837 29.41393 19.95945 |
|
15bbd86c6c7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
23
diff
changeset
|
520 chr18 189223 189652 19.95945 12.60597 11.55547 23.11095 |
|
15bbd86c6c7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
23
diff
changeset
|
521 chr18 215232 216063 11.55547 15.75746 31.51493 72.48434 |
|
15bbd86c6c7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
23
diff
changeset
|
522 chr18 311530 312172 17.85846 11.55547 54.62588 43.07040 |
|
15bbd86c6c7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
23
diff
changeset
|
523 chr18 346464 347342 75.63583 40.96941 21.00995 16.80796 |
|
15bbd86c6c7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
23
diff
changeset
|
524 chr18 356560 357362 11.55547 14.70696 57.77737 53.57538 |
|
15bbd86c6c7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
23
diff
changeset
|
525 chr18 371110 372102 8.403982 9.454479 81.93882 82.98932 |
|
15bbd86c6c7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
23
diff
changeset
|
526 chr18 394600 396513 56.72687 43.07040 510.5419 438.0575 |
|
15bbd86c6c7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
23
diff
changeset
|
527 chr18 399014 400382 156.5241 117.6557 558.8648 496.8854 |
|
15bbd86c6c7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
23
diff
changeset
|
528 chr18 498906 500200 767.9138 278.3819 196.4430 181.7361 |
|
15bbd86c6c7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
23
diff
changeset
|
529 ===== ====== ====== ========= ========= ========== ========== |
|
22
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
|
530 |
|
23
393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
22
diff
changeset
|
531 ----- |
|
22
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
|
532 |
|
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
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changeset
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533 **More Information** |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
|
534 |
|
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
|
535 Generally, processing data with DiffBind involves five phases: |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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changeset
|
536 |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
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changeset
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537 #. Reading in peaksets |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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changeset
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538 #. Occupancy analysis |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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539 #. Counting reads |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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540 #. Differential binding affinity analysis |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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541 #. Plotting and reporting |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
|
542 |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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changeset
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543 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
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changeset
|
544 **Reading in peaksets**: |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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545 |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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546 The first step is to read in a set of peaksets and associated |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
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547 metadata. Peaksets are derived either from ChIP-Seq peak callers, such as **MACS2**, or using some other criterion (e.g. genomic windows, or all the promoter regions |
|
393393c58c35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
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parents:
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548 in a genome). A single experiment can have more than |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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549 one associated peakset; e.g. if multiple peak callers are used for comparison purposes |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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550 each sample would have more than one line in the sample sheet. Once the peaksets |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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551 are read in, a merging function finds all overlapping peaks and derives a single set of |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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552 unique genomic intervals covering all the supplied peaks (a consensus peakset for the |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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553 experiment). |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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554 |
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555 **Occupancy analysis**: |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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556 |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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557 Peaksets, especially those generated by peak callers, provide |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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558 an insight into the potential occupancy of the protein being ChIPed for at specific |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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559 genomic loci. After the peaksets have been loaded, it can be useful to perform some |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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560 exploratory plotting to determine how these occupancy maps agree with each other, |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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561 e.g. between experimental replicates (re-doing the ChIP under the same conditions), |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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562 between different peak callers on the same experiment, and within groups of samples |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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563 representing a common experimental condition. DiffBind provides functions to enable |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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564 overlaps to be examined, as well as functions to determine how well similar samples |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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changeset
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565 cluster together. Beyond quality control, the product of an occupancy analysis may be |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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changeset
|
566 a consensus peakset, representing an overall set of candidate binding sites to be used |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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567 in further analysis. |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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568 |
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569 **Counting reads**: |
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|
570 |
|
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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571 Once a consensus peakset has been derived, DiffBind can use the |
|
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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572 supplied sequence read files to count how many reads overlap each interval for each |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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changeset
|
573 unique sample. The peaks in the consensus peakset may be re-centered and trimmed |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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574 based on calculating their summits (point of greatest read overlap) in order to provide |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
|
575 more standardized peak intervals. The final result of counting is a binding affinity matrix |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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576 containing a (normalized) read count for each sample at every potential binding site. |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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changeset
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577 With this matrix, the samples can be re-clustered using affinity, rather than occupancy, |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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578 data. The binding affinity matrix is used for QC plotting as well as for subsequent |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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579 differential analysis. |
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51f0f4df83c2
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580 |
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581 **Differential binding affinity analysis**: |
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582 |
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51f0f4df83c2
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583 The core functionality of DiffBind is the |
|
51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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584 differential binding affinity analysis, which enables binding sites to be identified that |
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51f0f4df83c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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585 are statistically significantly differentially bound between sample groups. To accomplish |
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586 this, first a contrast (or contrasts) is established, dividing the samples into groups to |
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587 be compared. Next the core analysis routines are executed, by default using DESeq2. |
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588 This will assign a p-value and FDR to each candidate binding site indicating confidence |
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589 that they are differentially bound. |
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590 |
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591 **Plotting and reporting**: |
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592 |
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51f0f4df83c2
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593 Once one or more contrasts have been run, DiffBind provides |
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594 a number of functions for reporting and plotting the results. MA plots give an |
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51f0f4df83c2
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595 overview of the results of the analysis, while correlation heatmaps and PCA plots show |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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596 how the groups cluster based on differentially bound sites. Boxplots show the distribution |
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597 of reads within differentially bound sites corresponding to whether they gain or |
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598 lose affinity between the two sample groups. A reporting mechanism enables differentially |
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599 bound sites to be extracted for further processing, such as annotation, motif, and |
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600 pathway analyses. |
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601 |
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602 ----- |
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603 |
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604 **References** |
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605 |
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606 DiffBind Authors: Rory Stark, Gordon Brown (2011) |
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607 Wrapper authors: Bjoern Gruening, Pavankumar Videm |
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608 |
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609 .. _DiffBind: https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
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610 .. _`Bioconductor package`: https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
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611 .. _`DiffBind User Guide`: https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf |
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612 .. _`Bioconductor post`: https://support.bioconductor.org/p/69924/ |
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613 .. _here: https://galaxyproject.org/learn/datatypes/#interval |
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614 .. _`Biostars post`: https://www.biostars.org/p/84686/ |
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615 |
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616 ]]> |
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617 </help> |
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618 <citations> |
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619 <citation type="doi">doi:10.1038/nature10730</citation> |
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620 </citations> |
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621 </tool> |