splice_site_summary.pl - Find novel splice junctions in RNA-seq data.
splice_site_summary.pl [-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 <email@example.com>