NAME - Produce BED12 from BED6 splice junction files.

SYNOPSIS [-s FILE] [options]


Convert splice junctions from mapped RNA-seq data to BED12 format for easy genome browser visualization. The program expects BED6 input in segemehl splice junction format (see the segemehl documentation for details) and produces BED12 and optionally bigBed output.



Splice junctions from mapped RNA-seq data in BED6 format


Chromosome sizes files


Convert resuting BED6 files to bigBed format


Minimum read coverage for a splice junction. Only splice junctions that are supported by at least this number of reads are considered.


Expand splice junctions by a window of this size on both sides


Filter circular splice junctions


Relative output path

--help -h

Print short help


Prints the manual page and exits


Michael T. Wolfinger <>