rseqc: read_NVC.xml annotate

annotate read_NVC.xml @ 33:073c77ce5e94

export PYTHONPATH during install, note python 2.7 requirement

author	lparsons
date	Tue, 15 Oct 2013 12:58:55 -0400
parents	580ee0c4bc4e
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_read_NVC" name="Read NVC" 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>to check the nucleotide composition bias</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>
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	9 read_NVC.py -i $input -o output $nx
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 </command>
31 cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	11 <stdio>
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	12 <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	13 <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	14 </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	15 <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	16 <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	17 <param name="nx" type="boolean" value="false" truevalue="-x" falsevalue="" label="Include N,X in NVC plot"/>
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 </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	19 <outputs>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	20 <data format="xls" name="outputxls" from_work_dir="output.NVC.xls" label="${tool.name} on ${on_string} (XLS)" />
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	21 <data format="txt" name="outputr" from_work_dir="output.NVC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	22 <data format="pdf" name="outputpdf" from_work_dir="output.NVC_plot.pdf" label="${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	23 </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	24 <help>
31 cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	25 read_NVC.py
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	26 +++++++++++
907d4b021ff6 Uploaded nilesh parents: diff changeset	27
31 cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	28 This module is used to check the nucleotide composition bias. Due to random priming, certain
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	29 patterns are over represented at the beginning (5'end) of reads. This bias could be easily
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	30 examined by NVC (Nucleotide versus cycle) plot. NVC plot is generated by overlaying all
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	31 reads together, then calculating nucleotide composition for each position of read
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	32 (or each sequencing cycle). In ideal condition (genome is random and RNA-seq reads is
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	33 randomly sampled from genome), we expect A%=C%=G%=T%=25% at each position of reads.
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	34
31 cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	35 NOTE: this program expect a fixed read length
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	36
907d4b021ff6 Uploaded nilesh parents: diff changeset	37 Inputs
907d4b021ff6 Uploaded nilesh parents: diff changeset	38 ++++++++++++++
907d4b021ff6 Uploaded nilesh parents: diff changeset	39
907d4b021ff6 Uploaded nilesh parents: diff changeset	40 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	41 Alignment file in BAM/SAM format.
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	42
907d4b021ff6 Uploaded nilesh parents: diff changeset	43 Include N,X in NVC plot
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	44 Plots N and X alongside A, T, C, and G in plot.
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	45
907d4b021ff6 Uploaded nilesh parents: diff changeset	46 Output
907d4b021ff6 Uploaded nilesh parents: diff changeset	47 ++++++++++++++
907d4b021ff6 Uploaded nilesh parents: diff changeset	48
907d4b021ff6 Uploaded nilesh parents: diff changeset	49 This module is used to check the nucleotide composition bias. Due to random priming, certain patterns are over represented at the beginning (5'end) of reads. This bias could be easily examined by NVC (Nucleotide versus cycle) plot. NVC plot is generated by overlaying all reads together, then calculating nucleotide composition for each position of read (or each sequencing cycle). In ideal condition (genome is random and RNA-seq reads is randomly sampled from genome), we expect A%=C%=G%=T%=25% at each position of reads.
907d4b021ff6 Uploaded nilesh parents: diff changeset	50
907d4b021ff6 Uploaded nilesh parents: diff changeset	51
907d4b021ff6 Uploaded nilesh parents: diff changeset	52 1. output.NVC.xls: plain text file, each row is position of read (or sequencing cycle), each column is nucleotide (A,C,G,T,N,X)
907d4b021ff6 Uploaded nilesh parents: diff changeset	53 2. output.NVC_plot.r: R script to generate NVC plot.
907d4b021ff6 Uploaded nilesh parents: diff changeset	54 3. output.NVC_plot.pdf: NVC plot.
907d4b021ff6 Uploaded nilesh parents: diff changeset	55
907d4b021ff6 Uploaded nilesh parents: diff changeset	56
31 cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	57 .. image:: http://rseqc.sourceforge.net/_images/NVC_plot.png
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	58 :height: 600 px
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	59 :width: 600 px
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	60 :scale: 80 %
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	61
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	62 -----
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	63
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	64 About RSeQC
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	65 +++++++++++
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	66
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	67 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	68
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	69 The RSeQC package is licensed under the GNU GPL v3 license.
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	70
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	71 .. image:: http://rseqc.sourceforge.net/_static/logo.png
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	72
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	73 .. _RSeQC: http://rseqc.sourceforge.net/
cc5eaa9376d8 Lance's updates nilesh parents: 29 diff changeset	74
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	75
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	76 </help>
29 907d4b021ff6 Uploaded nilesh parents: diff changeset	77 </tool>

Mercurial > repos > nilesh > rseqc

annotate read_NVC.xml @ 33:073c77ce5e94