Mercurial > repos > nilesh > rseqc
annotate read_NVC.xml @ 35:ff21a055413b
Create lib directories during install, added README.txt
| author | lparsons |
|---|---|
| date | Tue, 22 Jul 2014 16:52:10 -0400 |
| parents | 580ee0c4bc4e |
| children |
| rev | line source |
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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
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1 <tool id="rseqc_read_NVC" name="Read NVC" version="1.1"> |
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580ee0c4bc4e
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2 <description>to check the nucleotide composition bias</description> |
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580ee0c4bc4e
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3 <requirements> |
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4 <requirement type="package" version="3.0.1">R</requirement> |
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5 <requirement type="package" version="1.7.1">numpy</requirement> |
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6 <requirement type="package" version="2.3.7">rseqc</requirement> |
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580ee0c4bc4e
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7 </requirements> |
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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
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8 <command> |
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580ee0c4bc4e
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9 read_NVC.py -i $input -o output $nx |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
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10 </command> |
| 31 | 11 <stdio> |
| 12 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> | |
| 13 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> | |
| 14 </stdio> | |
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15 <inputs> |
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580ee0c4bc4e
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16 <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> |
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580ee0c4bc4e
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17 <param name="nx" type="boolean" value="false" truevalue="-x" falsevalue="" label="Include N,X in NVC plot"/> |
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580ee0c4bc4e
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18 </inputs> |
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580ee0c4bc4e
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19 <outputs> |
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20 <data format="xls" name="outputxls" from_work_dir="output.NVC.xls" label="${tool.name} on ${on_string} (XLS)" /> |
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580ee0c4bc4e
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lparsons
parents:
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21 <data format="txt" name="outputr" from_work_dir="output.NVC_plot.r" label="${tool.name} on ${on_string} (R Script)" /> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
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22 <data format="pdf" name="outputpdf" from_work_dir="output.NVC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" /> |
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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:
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23 </outputs> |
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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:
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24 <help> |
| 31 | 25 read_NVC.py |
| 29 | 26 +++++++++++ |
| 27 | |
| 31 | 28 This module is used to check the nucleotide composition bias. Due to random priming, certain |
| 29 patterns are over represented at the beginning (5'end) of reads. This bias could be easily | |
| 30 examined by NVC (Nucleotide versus cycle) plot. NVC plot is generated by overlaying all | |
| 31 reads together, then calculating nucleotide composition for each position of read | |
| 32 (or each sequencing cycle). In ideal condition (genome is random and RNA-seq reads is | |
| 33 randomly sampled from genome), we expect A%=C%=G%=T%=25% at each position of reads. | |
| 29 | 34 |
| 31 | 35 NOTE: this program expect a fixed read length |
| 29 | 36 |
| 37 Inputs | |
| 38 ++++++++++++++ | |
| 39 | |
| 40 Input BAM/SAM file | |
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41 Alignment file in BAM/SAM format. |
| 29 | 42 |
| 43 Include N,X in NVC plot | |
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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:
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44 Plots N and X alongside A, T, C, and G in plot. |
| 29 | 45 |
| 46 Output | |
| 47 ++++++++++++++ | |
| 48 | |
| 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. | |
| 50 | |
| 51 | |
| 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) | |
| 53 2. output.NVC_plot.r: R script to generate NVC plot. | |
| 54 3. output.NVC_plot.pdf: NVC plot. | |
| 55 | |
| 56 | |
| 31 | 57 .. image:: http://rseqc.sourceforge.net/_images/NVC_plot.png |
| 58 :height: 600 px | |
| 59 :width: 600 px | |
| 60 :scale: 80 % | |
| 61 | |
| 62 ----- | |
| 63 | |
| 64 About RSeQC | |
| 65 +++++++++++ | |
| 66 | |
| 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. | |
| 68 | |
| 69 The RSeQC package is licensed under the GNU GPL v3 license. | |
| 70 | |
| 71 .. image:: http://rseqc.sourceforge.net/_static/logo.png | |
| 72 | |
| 73 .. _RSeQC: http://rseqc.sourceforge.net/ | |
| 74 | |
| 29 | 75 |
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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
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76 </help> |
| 29 | 77 </tool> |