# HG changeset patch
# User devteam
# Date 1444754330 14400
# Node ID d0969fa24eb1d919cd2ce5e72c1602d27e21b775
# Parent 20e471a2fdc6d90fff5ab1a857bb62c30ecf26ec
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
diff -r 20e471a2fdc6 -r d0969fa24eb1 fasta_clipping_histogram.xml
--- a/fasta_clipping_histogram.xml Tue Jun 03 15:30:44 2014 -0400
+++ b/fasta_clipping_histogram.xml Tue Oct 13 12:38:50 2015 -0400
@@ -1,19 +1,20 @@
- chart
+ chart
fastx_toolkit
- fasta_clipping_histogram.pl $input $outfile
-
-
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-
+ fasta_clipping_histogram.pl $input $outfile
+
+
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-
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**What it does**
This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file.
@@ -24,21 +25,18 @@
**Output Examples**
-In the following library, most sequences are 24-mers to 27-mers.
+In the following library, most sequences are 24-mers to 27-mers.
This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place).
.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_1.png
-
-In the following library, most sequences are 19,22 or 23-mers.
+In the following library, most sequences are 19,22 or 23-mers.
This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place).
.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_2.png
-
-----
-
**Input Formats**
This tool accepts short-reads FASTA files. The reads don't have to be short, but they do have to be on a single line, like so::
@@ -50,7 +48,6 @@
>sequence3
CCTTGAGATTAACGCTAATCAAGTAAAC
-
If the sequences span over multiple lines::
>sequence1
@@ -63,11 +60,8 @@
>sequence1
CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
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-----
-
-
**Multiplicity counts (a.k.a reads-count)**
If the sequence identifier (the text after the '>') contains a dash and a number, it is treated as a multiplicity count value (i.e. how many times that individual sequence repeated in the original FASTA file, before collapsing).
@@ -85,7 +79,6 @@
.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_3.png
-
Example 2 - The following FASTA file have multiplicity counts::
>seq1-2
@@ -106,7 +99,5 @@
This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
.. __: http://hannonlab.cshl.edu/fastx_toolkit/
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\ No newline at end of file
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+
diff -r 20e471a2fdc6 -r d0969fa24eb1 fasta_clipping_histogram_1.png
Binary file fasta_clipping_histogram_1.png has changed
diff -r 20e471a2fdc6 -r d0969fa24eb1 fasta_clipping_histogram_2.png
Binary file fasta_clipping_histogram_2.png has changed
diff -r 20e471a2fdc6 -r d0969fa24eb1 fasta_clipping_histogram_3.png
Binary file fasta_clipping_histogram_3.png has changed
diff -r 20e471a2fdc6 -r d0969fa24eb1 fasta_clipping_histogram_4.png
Binary file fasta_clipping_histogram_4.png has changed
diff -r 20e471a2fdc6 -r d0969fa24eb1 tool_dependencies.xml
--- a/tool_dependencies.xml Tue Jun 03 15:30:44 2014 -0400
+++ b/tool_dependencies.xml Tue Oct 13 12:38:50 2015 -0400
@@ -1,6 +1,6 @@
-
+