NAME

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

SYNOPSIS

sj_visualizer.pl [-s FILE] [-f FILE] [options]

DESCRIPTION

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

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>