sj_visualizer.pl - Produce BED12 from BED6 splice junction files.
sj_visualizer.pl [-s FILE] [options]
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.
Splice junctions from mapped RNA-seq data in BED6 format
Chromosome sizes files
Convert resuting BED6 files to bigBed format
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
Filter circular splice junctions
Relative output path
Print short help
Prints the manual page and exits
Michael T. Wolfinger <michael@wolfinger.eu>
To install Bio::ViennaNGS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::ViennaNGS
CPAN shell
perl -MCPAN -e shell install Bio::ViennaNGS
For more information on module installation, please visit the detailed CPAN module installation guide.