changeset 10:1ce3d6f45fbc draft

Uploaded

--- a/rgrnastar/rg_rnaStar.xml	Sat Aug 10 08:58:12 2013 -0400
+++ b/rgrnastar/rg_rnaStar.xml	Mon Aug 12 05:07:28 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="rna_star" name="RNA-STAR" version="0.21">
+<tool id="rna_star" name="RNA-STAR" version="0.22">
     <description>Gapped-read mapper for RNA-seq data</description>
     <requirements>
         <requirement type="package" version="2.3.0e">rnastar</requirement>
@@ -22,13 +22,14 @@
         --runThreadN 4
 
     ## Parameters.
+    --outSAMattributes "$outSAMattributes"
     #if $params.settingsType == "full":
         --chimSegmentMin $params.chim_segment_min
         --chimScoreMin $params.chim_score_min
     #end if
 
-    ## Needed to generate SAM tags for Cufflinks tools.
-    --outSAMstrandField intronMotif
+    ## may or may not need to generate SAM tags and handle non-canonicals for Cufflinks tools.
+    ${outSAMstrandField} $outFilterIntronMotifs}
 
     ;
 
@@ -89,7 +90,19 @@
                 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
             </when>
         </conditional>
-
+            <param name="outSAMattributes" type="select" label="Include extra sam attributes for downstream processing">
+              <option value="Standard">Standard - eg for old Samtools downstream</option>
+              <option value="All" selected="true">All modern Samtools attributes - see below</option>
+            </param>
+            <param name="outSAMstrandField" type="select" label="Include extra sam attributes for downstream processing">
+              <option value="--outSAMstrandField intronMotif" selected="true">Add XS for cufflinks</option>
+              <option value="">No XS added to sam output</option>
+            </param>
+            <param name="outFilterIntronMotifs" type="select" label="Canonical junction preparation for unstranded data">
+              <option value="">No special handling - all non-canonical junctions passed through</option>
+              <option value="--outFilterIntronMotifs RemoveNoncanonical" selected="true">Remove all non-canonical junctions for eg cufflinks</option>
+              <option value="--outFilterIntronMotifs RemoveNoncanonicalUnannotated">Remove only unannotated non-canonical junctions for eg cufflinks</option>
+            </param>
         <!-- Parameter settings. -->
         <conditional name="params">
             <param name="settingsType" type="select" label="Settings to use" help="You can use the default settings or set custom values for any STAR parameter.">
@@ -101,6 +114,7 @@
             <when value="full">
             <param name="chim_segment_min" type="integer" min="0" value="0" label="Minimum chimeric segment length" />
             <param name="chim_score_min" type="integer" min="0" value="0" label="Minimum total (summed) score of the chimeric segments" />
+
             </when>
         </conditional>
     </inputs>
@@ -189,6 +203,61 @@
         </data>
     </outputs>
 <help>
+
+**What it does**
+Runs the rna star gapped aligner. Suited to paired or single end rna-seq.
+
+8.2: SAM alignments
+
+The number of loci Nmap a read maps to (multi-mapping) is given by NH:i: field.
+The mapping quality MAPQ (column 5) is 255 for uniquely mapping reads, and int(-10*log10(1-1/Nmap)) for
+multi-mapping reads. This scheme is same as the one used by Tophat and is compatible with Cufflinks.
+
+For multi-mappers, all alignments except one are marked with 0x100 (secondary alignment) in the FLAG
+column 2. The un-marked alignment is either the best one (i.e. highest scoring), or is randomly selected from
+the alignments of equal quality.
+
+8.2.1: Standard SAM attributes
+With default --outSAMattributes Standard option the following SAM attributes will be generated:
+
+Column 12: NH: number of loci a read (pair) maps to
+Column 13: IH: alignment index for all alignments of a read
+Column 14: aS: alignment score
+Column 15: nM: number of mismatches (does not include indels)
+
+8.2.2: Extra SAM attrbiutes
+If --outSAMattributes All option is used, the following additional attributes will be output:
+
+Column 16: jM:B:c,M1,M2,... Intron motifs for all junctions (i.e. N in CIGAR):
+0: non-canonical; 1:GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT.
+
+If splice junctions database is used, and a junction is annotated, 20 is added to its motif value.
+Column 17: jI:B:I,Start1,End1,Start2,End2,... Start and End of introns for all junctions (1-based)
+
+Note, that samtools 0.1.18 or later have to be used with these extra attributes.
+
+
+8.2.3: XS SAM strand attribute for Cufflinks/Cuffdiff
+
+If you have un-stranded RNA-seq data, and wish to run Cufflinks/Cuffdiff on STAR alignments, you will
+need to run STAR with --outSAMstrandField intronMotif option, which will generate the XS
+strand attribute for all alignments that contain splice junctions. The spliced alignments that have undefined
+strand (i.e. containing only non-canonical junctions) will be suppressed.
+
+If you have stranded RNA-seq data, you do not need to use any specific STAR options. Instead, you need
+to run Cufflinks with the library option --library-type options. For example, cufflinks <...> -
+library-type fr-firststrand should be used for the “standard” dUTP protocol. This option has
+to be used only for Cufflinks runs and not for STAR runs.
+
+It is recommended to remove the non-canonical junctions for Cufflinks runs using –
+--outFilterIntronMotifs RemoveNoncanonical
+filter out alignments that contain non-canonical junctions
+OR
+--outFilterIntronMotifs RemoveNoncanonicalUnannotated
+filter out alignments that contain non-canonical unannotated junctions
+when using annotated splice junctions database. The annotated non-
+canonical junctions will be kept.
+ 
     
 **Attributions**