# HG changeset patch
# User nilesh
# Date 1374164682 18000
# Node ID 8dab2cfd456f104ca4295534fdef0d234d695e4f
# Parent 0e4ef5fef2c517a1fbb7f6f7818436333f35ff5e
first commit
diff -r 0e4ef5fef2c5 -r 8dab2cfd456f .hgignore
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.hgignore Thu Jul 18 11:24:42 2013 -0500
@@ -0,0 +1,4 @@
+# use glob syntax
+syntax: regexp
+
+^test-data/.*
\ No newline at end of file
diff -r 0e4ef5fef2c5 -r 8dab2cfd456f RPKM_count.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RPKM_count.xml Thu Jul 18 11:24:42 2013 -0500
@@ -0,0 +1,110 @@
+
+ calculates raw count and RPKM values for transcript at exon, intron, and mRNA level
+
+ samtools
+ rseqc
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+ samtoolshelper.py RPKM_count.py -i $input -o output -r $refgene
+
+ #if $nx
+ -x
+ #end if
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+ #if str($strand_type.strand_specific) == "pair"
+ -d
+ #if str($strand_type.pair_type) == "sd"
+ '1++,1--,2+-,2-+'
+ #else
+ '1+-,1-+,2++,2--'
+ #end if
+ #end if
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+ #if str($strand_type.strand_specific) == "single"
+ -d
+ #if str($strand_type.single_type) == "s"
+ '++,--'
+ #else
+ '+-,-+'
+ #end if
+ #end if
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+ #if $skiphits
+ -u
+ #end if
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+ #if $onlyexonic
+ -e
+ #end if
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+.. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
+
+-----
+
+About RSeQC
++++++++++++
+
+The RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-seq specific modules” investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
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+The RSeQC package is licensed under the GNU GPL v3 license.
+
+Inputs
+++++++++++++++
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+Input BAM/SAM file
+ Alignment file in BAM/SAM format.
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+Reference gene model
+ Gene model in BED format.
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+Strand sequencing type (default=none)
+ See Infer Experiment tool if uncertain.
+
+Options
+++++++++++++++
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+Skip Multiple Hit Reads
+ Use Multiple hit reads or use only uniquely mapped reads.
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+Only use exonic reads
+ Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads.
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diff -r 0e4ef5fef2c5 -r 8dab2cfd456f RPKM_saturation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RPKM_saturation.xml Thu Jul 18 11:24:42 2013 -0500
@@ -0,0 +1,128 @@
+
+ calculates raw count and RPKM values for transcript at exon, intron, and mRNA level
+
+ R
+ rseqc
+
+ RPKM_saturation.py -i $input -o output -r $refgene
+
+ #if str($strand_type.strand_specific) == "pair"
+ -d
+ #if str($strand_type.pair_type) == "sd"
+ '1++,1--,2+-,2-+'
+ #else
+ '1+-,1-+,2++,2--'
+ #end if
+ #end if
+
+ #if str($strand_type.strand_specific) == "single"
+ -d
+ #if str($strand_type.single_type) == "s"
+ '++,--'
+ #else
+ '+-,-+'
+ #end if
+ #end if
+
+ -l $percentileFloor -u $percentileCeiling -s $percentileStep -c $rpkmCutoff
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