gtfutils / add_isoform

Adds isoform annotations to a GTF file (isoforms)

This adds isoform annotations based upon the KnownGene annotations from the
UCSC Genome Browser. Isoforms are taken from the knownIsoform table. This
table must be downloaded from the UCSC Genome Browser.

The isoforms file should be in the following format:

isoform_id {tab} transcript_id

Where all transcripts that are isoforms of the same gene will have the same
isoform_id value.

This will add the following attributes:
    isoform_id (isoform cluster id)

Usage: gtfutils add_isoform filename.gtf knownIsoform.txt