NAME

splice_site_summary.pl - Find novel splice junctions in RNA-seq data.

SYNOPSIS

splice_site_summary.pl [-s FILE] [-a FILE] [-f FILE] [options]

DESCRIPTION

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

OPTIONS

-a

Reference annotation in BED12 format

-s

Splice junctions from mapped RNA-seq data in BED6 format

-f

Reference genome in Fasta format

-c

Chromosome sizes files

-b

Convert resuting BED6 files to bigBed format

-n

Filter canonical splice junctions

-i

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

-r

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

-w

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

-o

Relative output path

-p

Prefix all output files with this string

--help -h

Print short help

--man

Prints the manual page and exits

AUTHOR

Michael T. Wolfinger <michael@wolfinger.eu>