jvarkit

FindNewSpliceSites

Last commit

use the ā€˜Nā€™ operator in the cigar string to find unknown splice sites

Usage

Usage: findnewsplicesites [options] Files
  Options:
    --bamcompression
      Compression Level.
      Default: 5
    -B, --bed
      Optional BED output
  * -g, --gtf
      A GTF file.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -out, --out
      Output file. Optional . Default: stdout
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    --version
      print version and exit
    -d
      max distance between known splice site and cigar end
      Default: 10

Keywords

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew findnewsplicesites

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/rnaseq/FindNewSpliceSites.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite findnewsplicesites ? 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

$  java -jar dist/findnewsplicesites.jar \
     --gtf http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.gtf.gz \
      hg19.bam > out.sam