Mercurial > repos > nilesh > rseqc
diff RPKM_count.xml @ 31:cc5eaa9376d8
Lance's updates
| author | nilesh |
|---|---|
| date | Wed, 02 Oct 2013 02:20:04 -0400 |
| parents | 907d4b021ff6 |
| children | 580ee0c4bc4e |
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--- a/RPKM_count.xml Thu Jul 11 12:33:27 2013 -0400 +++ b/RPKM_count.xml Wed Oct 02 02:20:04 2013 -0400 @@ -1,15 +1,14 @@ -<tool id="RPKM_count" name="RPKM Count"> +<tool id="RPKM_count" name="RPKM Count" version="1.1"> <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description> <requirements> - <requirement type="package" version="0.1.18">samtools</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> <requirement type="package" version="2.3.7">rseqc</requirement> </requirements> - <command interpreter="python"> samtoolshelper.py RPKM_count.py -i $input -o output -r $refgene + <command> + ln -s "${input}" "local_input.bam" && + ln -s "${input.metadata.bam_index}" "local_input.bam.bai" && + RPKM_count.py -i "local_input.bam" -o output -r $refgene - #if $nx - -x - #end if - #if str($strand_type.strand_specific) == "pair" -d #if str($strand_type.pair_type) == "sd" @@ -66,17 +65,19 @@ <outputs> <data format="xls" name="outputxls" from_work_dir="output_read_count.xls"/> </outputs> + <stdio> + <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> + <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> + </stdio> <help> -.. image:: https://code.google.com/p/rseqc/logo?cct=1336721062 - ------ +RPKM_count.py ++++++++++++++ -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. - -The RSeQC package is licensed under the GNU GPL v3 license. +Given a BAM file and reference gene model, this program will calculate the raw count and RPKM +values for transcript at exon, intron and mRNA level. For strand specific RNA-seq data, +program will assign read to its parental gene according to strand rule, if you don't know the +strand rule, run infer_experiment.py. Please note that chromosome ID, genome cooridinates +should be concordant between BAM and BED files. Inputs ++++++++++++++ @@ -102,46 +103,30 @@ Sample Output ++++++++++++++ -===== ===== === ========= ===== =========== ============= ============= ======== ======== -chrom start end accession score gene strand tag count (+) tag count (-) RPKM (+) RPKM (-) -===== ===== === ========= ===== =========== ============= ============= ======== ======== -chr1 29213722 29313959 NM_001166007_intron_1 0 + 431 4329 0.086 0.863 -chr1 29314417 29319841 NM_001166007_intron_2 0 + 31 1 0.114 0.004 -chr1 29320054 29323726 NM_001166007_intron_3 0 + 32 0 0.174 0 -chr1 29323831 29338376 NM_001166007_intron_4 0 + 33 2 0.045 0.003 -chr1 29338419 29342203 NM_001166007_intron_5 0 + 7 0 0.037 0 -chr1 29342279 29344735 NM_001166007_intron_6 0 + 35 4 0.285 0.033 -chr1 29344954 29356911 NM_001166007_intron_7 0 + 34 2 0.057 0.003 -chr1 29356999 29359604 NM_001166007_intron_8 0 + 19 1 0.146 0.008 -chr1 29359757 29362337 NM_001166007_intron_9 0 + 31 0 0.24 0 -chr1 29362435 29365765 NM_001166007_intron_10 0 + 11 1 0.066 0.006 -chr1 29365938 29379615 NM_001166007_intron_11 0 + 63 0 0.092 0 -chr1 29379824 29391493 NM_001166007_intron_12 0 + 383 8 0.656 0.014 -chr1 29391670 29424318 NM_001166007_intron_13 0 + 817 10 0.5 0.006 -chr1 29424447 29435847 NM_001166007_intron_14 0 + 28 0 0.049 0 -chr1 29435949 29438879 NM_001166007_intron_15 0 + 12 0 0.082 0 -chr1 29438960 29442210 NM_001166007_intron_16 0 + 22 2 0.135 0.012 -chr1 29442315 29443330 NM_001166007_intron_17 0 + 9 0 0.177 0 -chr1 29213602 29213722 NM_001166007_exon_1 0 + 164 0 27.321 0 -chr1 29313959 29314417 NM_001166007_exon_2 0 + 1699 4 74.158 0.175 -chr1 29319841 29320054 NM_001166007_exon_3 0 + 528 1 49.554 0.094 -chr1 29323726 29323831 NM_001166007_exon_4 0 + 168 0 31.985 0 -chr1 29338376 29338419 NM_001166007_exon_5 0 + 88 0 40.911 0 -chr1 29342203 29342279 NM_001166007_exon_6 0 + 114 3 29.986 0.789 -chr1 29344735 29344954 NM_001166007_exon_7 0 + 290 10 26.472 0.913 -chr1 29356911 29356999 NM_001166007_exon_8 0 + 146 1 33.166 0.227 -chr1 29359604 29359757 NM_001166007_exon_9 0 + 404 11 52.786 1.437 -chr1 29362337 29362435 NM_001166007_exon_10 0 + 85 7 17.339 1.428 -chr1 29365765 29365938 NM_001166007_exon_11 0 + 198 2 22.88 0.231 -chr1 29379615 29379824 NM_001166007_exon_12 0 + 306 5 29.269 0.478 -chr1 29391493 29391670 NM_001166007_exon_13 0 + 243 7 27.445 0.791 -chr1 29424318 29424447 NM_001166007_exon_14 0 + 298 7 46.18 1.085 -chr1 29435847 29435949 NM_001166007_exon_15 0 + 396 8 77.611 1.568 -chr1 29438879 29438960 NM_001166007_exon_16 0 + 307 0 75.767 0 -chr1 29442210 29442315 NM_001166007_exon_17 0 + 138 0 26.273 0 -chr1 29443330 29446558 NM_001166007_exon_18 0 + 2434 84 15.074 0.52 -chr1 29213602 29446558 NM_001166007_mRNA 0 + 8006 150 27.704 0.519 -===== ===== === ========= ===== =========== ============= ============= ======== ======== +===== ======== ======== ===================== ===== =========== ============= ============= ======== ========= +chrom start end accession score gene strand tag count (+) tag count (-) RPKM (+) RPKM (-) +===== ======== ======== ===================== ===== =========== ============= ============= ======== ========= +chr1 29213722 29313959 NM_001166007_intron_1 0 '+' 431 4329 0.086 0.863 +chr1 29314417 29319841 NM_001166007_intron_2 0 '+' 31 1 0.114 0.004 +chr1 29320054 29323726 NM_001166007_intron_3 0 '+' 32 0 0.174 0.000 +chr1 29213602 29213722 NM_001166007_exon_1 0 '+' 164 0 27.321 0.000 +chr1 29313959 29314417 NM_001166007_exon_2 0 '+' 1699 4 74.158 0.175 +chr1 29319841 29320054 NM_001166007_exon_3 0 '+' 528 1 49.554 0.094 +===== ======== ======== ===================== ===== =========== ============= ============= ======== ========= +----- + +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. + +The RSeQC package is licensed under the GNU GPL v3 license. + +.. image:: http://rseqc.sourceforge.net/_static/logo.png + +.. _RSeQC: http://rseqc.sourceforge.net/ + + </help> </tool>