jvarkit

Biostar103303

Calculate Percent Spliced In (PSI).

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar biostar103303  [options] Files

Usage: biostar103303 [options] Files
  Options:
  * -g, --gtf
      GTF file.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• sam
• bam
• psi

See also in Biostars

• https://www.biostars.org/p/103303

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar103303.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite biostar103303 ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

##Example

$   curl -s "http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqA549CellLongnonpolyaAlnRep1.bam" |\
  java -jar dist/biostar103303.jar -g "http://atgu.mgh.harvard.edu/plinkseq/dist/aux/gencodeBasicV11-hg19.gtf.gz"  > result.tsv

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