Splice2bed module

This module allow to convert a SAM file into a BED file and keep splicing information. If a "TrackColor" column is defined in the design file, the BED entries will use the color defined for the related sample. In other cases, BED entries will be colored against the mapped strand.

  • Internal name: splice2bed
  • Available: Both local and distributed mode

  • Input port:
    • input: data to convert (in SAM format)

  • Output ports:
    • output: converted data (in BED format)

  • Mandatory parameter: None

  • Optional parameter: None
  • Configuration example:
  • <!-- Create BED with splicings step -->
    <step id="mysplice2bedstep" skip="false" discardoutput="false">