Extract splice junctions from TALON DB or GTF

Obtaining a table of splice junctions from your TALON database (or TALON GTF)

After running TALON, you may want to examine splice junction usage. To do so, we have provided a tool to extract splice junctions from a TALON database. Additionally, this tool can be used to extract splice junctions from a GTF, in case you want to first filter your transcript models before running this utility.

Note that this takes in either a TALON database or TALON GTF, not both!

talon_get_sjs --h

Usage: talon_get_sjs [options]

Options: 
  -h, --help            show this help message and exit
  --gtf                 TALON GTF file from which to extract exons/introns
  --db                  TALON database from which to extract exons/introns
  --ref                 GTF reference file (ie GENCODE). Will be used to label
                        novelty.
  --mode                Choices are 'intron' or 'exon' (default is 'intron').
                        Determines whether to include introns or exons in the
                        output
  --outprefix           Prefix for output file