rseqc: junction_saturation.xml annotate

annotate junction_saturation.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_junction_saturation" name="Junction Saturation" 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>detects splice junctions from each subset and compares them to reference gene model</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="3.0.1">R</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="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	6 <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	7 </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	8 <command> junction_saturation.py -i $input -o output -r $refgene -m $intronSize -v $minSplice
22 d064a3014efd Uploaded nilesh parents: diff changeset	9
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	10 #if $percentiles.specifyPercentiles
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	11 -l $percentiles.lowBound -u $percentiles.upBound -s $percentiles.percentileStep
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 #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	13
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 </command>
31 cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	15 <stdio>
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	16 <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: 22 diff changeset	17 <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: 22 diff changeset	18 </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	19 <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	20 <param name="input" type="data" format="bam,sam" 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	21 <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	22 <param name="intronSize" type="integer" label="Minimum intron size (bp, default=50)" value="50"/>
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 <param name="minSplice" type="integer" label="Minimum coverage (default=1)" value="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	24 <conditional name="percentiles">
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 <param name="specifyPercentiles" type="boolean" label="Specify sampling bounds and frequency" value="false"/>
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 <when value="true">
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 <param name="lowBound" type="integer" value="5" label="Lower Bound Sampling Frequency (bp, default=5)" />
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 <param name="upBound" type="integer" value="100" label="Upper Bound Sampling Frequency (bp, default=100)" />
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 <param name="percentileStep" type="integer" value="5" label="Sampling increment (default=5)" />
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 </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	31 </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	32 </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	33 <outputs>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	34 <data format="txt" name="outputr" from_work_dir="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string} (R Script)"/>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	35 <data format="pdf" name="outputpdf" from_work_dir="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string} (PDF)"/>
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 </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	37 <help>
31 cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	38 junction_saturation.py
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	39 ++++++++++++++++++++++
22 d064a3014efd Uploaded nilesh parents: diff changeset	40
31 cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	41 It's very important to check if current sequencing depth is deep enough to perform
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	42 alternative splicing analyses. For a well annotated organism, the number of expressed genes
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	43 in particular tissue is almost fixed so the number of splice junctions is also fixed. The fixed
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	44 splice junctions can be predetermined from reference gene model. All (annotated) splice
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	45 junctions should be rediscovered from a saturated RNA-seq data, otherwise, downstream
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	46 alternative splicing analysis is problematic because low abundance splice junctions are
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	47 missing. This module checks for saturation by resampling 5%, 10%, 15%, ..., 95% of total
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	48 alignments from BAM or SAM file, and then detects splice junctions from each subset and
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	49 compares them to reference gene model.
22 d064a3014efd Uploaded nilesh parents: diff changeset	50
d064a3014efd Uploaded nilesh parents: diff changeset	51 Inputs
d064a3014efd Uploaded nilesh parents: diff changeset	52 ++++++++++++++
d064a3014efd Uploaded nilesh parents: diff changeset	53
d064a3014efd Uploaded nilesh parents: diff changeset	54 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	55 Alignment file in BAM/SAM format.
22 d064a3014efd Uploaded nilesh parents: diff changeset	56
d064a3014efd Uploaded nilesh parents: diff changeset	57 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	58 Gene model in BED format.
22 d064a3014efd Uploaded nilesh parents: diff changeset	59
d064a3014efd Uploaded nilesh parents: diff changeset	60 Sampling Percentiles - Upper Bound, Lower Bound, Sampling Increment (defaults= 100, 5, and 5)
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	61 Sampling starts from the Lower Bound and increments to the Upper Bound at the rate of the Sampling Increment.
22 d064a3014efd Uploaded nilesh parents: diff changeset	62
d064a3014efd Uploaded nilesh parents: diff changeset	63 Minimum intron length (default=50)
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	64 Minimum intron length (bp).
22 d064a3014efd Uploaded nilesh parents: diff changeset	65
d064a3014efd Uploaded nilesh parents: diff changeset	66 Minimum coverage (default=1)
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	67 Minimum number of supportting reads to call a junction.
22 d064a3014efd Uploaded nilesh parents: diff changeset	68
d064a3014efd Uploaded nilesh parents: diff changeset	69 Output
d064a3014efd Uploaded nilesh parents: diff changeset	70 ++++++++++++++
d064a3014efd Uploaded nilesh parents: diff changeset	71
d064a3014efd Uploaded nilesh parents: diff changeset	72 1. output.junctionSaturation_plot.r: R script to generate plot
d064a3014efd Uploaded nilesh parents: diff changeset	73 2. output.junctionSaturation_plot.pdf
d064a3014efd Uploaded nilesh parents: diff changeset	74
31 cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	75 .. image:: http://rseqc.sourceforge.net/_images/junction_saturation.png
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	76 :height: 600 px
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	77 :width: 600 px
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	78 :scale: 80 %
22 d064a3014efd Uploaded nilesh parents: diff changeset	79
d064a3014efd Uploaded nilesh parents: diff changeset	80 In this example, current sequencing depth is almost saturated for "known junction" (red line) detection because the number of "known junction" reaches a plateau. In other words, nearly all "known junctions" (expressed in this particular tissue) have already been detected, and continue sequencing will not detect additional "known junction" and will only increase junction coverage (i.e. junction covered by more reads). While current sequencing depth is not saturated for novel junctions (green).
d064a3014efd Uploaded nilesh parents: diff changeset	81
d064a3014efd Uploaded nilesh parents: diff changeset	82
31 cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	83 -----
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	84
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	85 About RSeQC
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	86 +++++++++++
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	87
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	88 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: 22 diff changeset	89
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	90 The RSeQC package is licensed under the GNU GPL v3 license.
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	91
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	92 .. image:: http://rseqc.sourceforge.net/_static/logo.png
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	93
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	94 .. _RSeQC: http://rseqc.sourceforge.net/
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	95
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	96
cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	97
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 </help>
31 cc5eaa9376d8 Lance's updates nilesh parents: 22 diff changeset	99 </tool>

Mercurial > repos > nilesh > rseqc

annotate junction_saturation.xml @ 32:580ee0c4bc4e