NAME

sj_visualizer.pl - Produce BED12 from BED6 splice junction files.

SYNOPSIS

sj_visualizer.pl [-s FILE] [options]

DESCRIPTION

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.

OPTIONS

-s

Splice junctions from mapped RNA-seq data in BED6 format

-c

Chromosome sizes files

-b

Convert resuting BED6 files to bigBed format

-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

-z

Filter circular splice junctions

-o

Relative output path

--help -h

Print short help

--man

Prints the manual page and exits

AUTHOR

Michael T. Wolfinger <michael@wolfinger.eu>