NAME - Find novel splice junctions in RNA-seq data.

SYNOPSIS [-s FILE] [-a FILE] [-f FILE] [options]


This program identifies and characterizes splice sites from mapped RNA-seq data against annotated splice junctions.



Reference annotation in BED12 format


Splice junctions from mapped RNA-seq data in BED6 format


Reference genome in Fasta format


Chromosome sizes files


Convert resuting BED6 files to bigBed format


Filter canonical splice junctions


Maximum intron length. Splice junctions covering introns larger than this value are not considered.


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


Relative output path


Prefix all output files with this string

--help -h

Print short help


Prints the manual page and exits


Michael T. Wolfinger <>