rseqc: RPKM_count.xml annotate

annotate RPKM_count.xml @ 32:580ee0c4bc4e

Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc

author	lparsons
date	Mon, 07 Oct 2013 15:01:13 -0400
parents	cc5eaa9376d8
children

rev	line source
32 580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	1 <tool id="rseqc_RPKM_count" name="RPKM Count" version="1.1">
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	2 <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	3 <requirements>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	4 <requirement type="package" version="1.7.1">numpy</requirement>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	5 <requirement type="package" version="2.3.7">rseqc</requirement>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	6 </requirements>
31 cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	7 <command>
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	8 ln -s "${input}" "local_input.bam" &&
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	9 ln -s "${input.metadata.bam_index}" "local_input.bam.bai" &&
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	10 RPKM_count.py -i "local_input.bam" -o output -r $refgene
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	11
32 580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	12 #if str($strand_type.strand_specific) == "pair"
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	13 -d
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	14 #if str($strand_type.pair_type) == "sd"
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	15 '1++,1--,2+-,2-+'
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	16 #else
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	17 '1+-,1-+,2++,2--'
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	18 #end if
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	19 #end if
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	20
32 580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	21 #if str($strand_type.strand_specific) == "single"
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	22 -d
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	23 #if str($strand_type.single_type) == "s"
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	24 '++,--'
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	25 #else
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	26 '+-,-+'
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	27 #end if
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	28 #end if
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	29
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	30 #if $skiphits
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	31 -u
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	32 #end if
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	33
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	34 #if $onlyexonic
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	35 -e
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	36 #end if
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	37
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	38 </command>
31 cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	39 <stdio>
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	40 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	41 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	42 </stdio>
32 580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	43 <inputs>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	44 <param name="input" type="data" format="bam" label="input bam/sam file" />
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	45 <param name="refgene" type="data" format="bed" label="Reference gene model" />
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	46 <conditional name="strand_type">
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	47 <param name="strand_specific" type="select" label="Strand-specific?" value="None">
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	48 <option value="none">None</option>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	49 <option value="pair">Pair-End RNA-seq</option>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	50 <option value="single">Single-End RNA-seq</option>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	51 </param>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	52 <when value="pair">
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	53 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd">
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	54 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	55 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	56 </param>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	57 </when>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	58 <when value="single">
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	59 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s">
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	60 <option value="s">positive --> positive; negative --> negative</option>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	61 <option value="d">positive --> negative; negative --> positive</option>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	62 </param>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	63 </when>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	64 <when value="none"></when>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	65 </conditional>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	66 <param name="skiphits" type="boolean" value="false" label="Skip Multiple Hit Reads" />
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	67 <param name="onlyexonic" type="boolean" value="false" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" />
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	68 </inputs>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	69 <outputs>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	70 <data format="xls" name="outputxls" from_work_dir="output_read_count.xls"/>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	71 </outputs>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	72 <help>
31 cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	73 RPKM_count.py
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	74 +++++++++++++
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	75
31 cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	76 Given a BAM file and reference gene model, this program will calculate the raw count and RPKM
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	77 values for transcript at exon, intron and mRNA level. For strand specific RNA-seq data,
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	78 program will assign read to its parental gene according to strand rule, if you don't know the
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	79 strand rule, run infer_experiment.py. Please note that chromosome ID, genome cooridinates
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	80 should be concordant between BAM and BED files.
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	81
907d4b021ff6 Uploaded nilesh parents: diff changeset	82 Inputs
907d4b021ff6 Uploaded nilesh parents: diff changeset	83 ++++++++++++++
907d4b021ff6 Uploaded nilesh parents: diff changeset	84
907d4b021ff6 Uploaded nilesh parents: diff changeset	85 Input BAM/SAM file
32 580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	86 Alignment file in BAM/SAM format.
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	87
907d4b021ff6 Uploaded nilesh parents: diff changeset	88 Reference gene model
32 580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	89 Gene model in BED format.
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	90
907d4b021ff6 Uploaded nilesh parents: diff changeset	91 Strand sequencing type (default=none)
32 580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	92 See Infer Experiment tool if uncertain.
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	93
907d4b021ff6 Uploaded nilesh parents: diff changeset	94 Options
907d4b021ff6 Uploaded nilesh parents: diff changeset	95 ++++++++++++++
907d4b021ff6 Uploaded nilesh parents: diff changeset	96
907d4b021ff6 Uploaded nilesh parents: diff changeset	97 Skip Multiple Hit Reads
32 580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	98 Use Multiple hit reads or use only uniquely mapped reads.
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	99
907d4b021ff6 Uploaded nilesh parents: diff changeset	100 Only use exonic reads
32 580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	101 Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads.
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	102
907d4b021ff6 Uploaded nilesh parents: diff changeset	103 Sample Output
907d4b021ff6 Uploaded nilesh parents: diff changeset	104 ++++++++++++++
907d4b021ff6 Uploaded nilesh parents: diff changeset	105
31 cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	106 ===== ======== ======== ===================== ===== =========== ============= ============= ======== =========
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	107 chrom start end accession score gene strand tag count (+) tag count (-) RPKM (+) RPKM (-)
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	108 ===== ======== ======== ===================== ===== =========== ============= ============= ======== =========
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	109 chr1 29213722 29313959 NM_001166007_intron_1 0 '+' 431 4329 0.086 0.863
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	110 chr1 29314417 29319841 NM_001166007_intron_2 0 '+' 31 1 0.114 0.004
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	111 chr1 29320054 29323726 NM_001166007_intron_3 0 '+' 32 0 0.174 0.000
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	112 chr1 29213602 29213722 NM_001166007_exon_1 0 '+' 164 0 27.321 0.000
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	113 chr1 29313959 29314417 NM_001166007_exon_2 0 '+' 1699 4 74.158 0.175
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	114 chr1 29319841 29320054 NM_001166007_exon_3 0 '+' 528 1 49.554 0.094
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	115 ===== ======== ======== ===================== ===== =========== ============= ============= ======== =========
32 580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	116
31 cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	117 -----
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	118
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	119 About RSeQC
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	120 +++++++++++
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	121
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	122 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.
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	123
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	124 The RSeQC package is licensed under the GNU GPL v3 license.
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	125
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	126 .. image:: http://rseqc.sourceforge.net/_static/logo.png
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	127
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	128 .. _RSeQC: http://rseqc.sourceforge.net/
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	129
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	130
32 580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	131 </help>
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	132 </tool>

Mercurial > repos > nilesh > rseqc

annotate RPKM_count.xml @ 32:580ee0c4bc4e