gtfutils / add_reflink

Adds gene name and isoform annotations to a GTF file (refLink)

This adds isoform and gene name annotations based upon the refLink table from
the UCSC Genome Browser. This assumes that the GTF transcript_id is the same
as the mrnaAcc field in the refLink table. Any transcripts with the same
locuslink/gene id will be treated as isoforms of each other.

This will add the following attributes:
    isoform_id (NCBI LocusLinkID/GeneID)

Usage: gtfutils add_reflink filename.gtf reflink.txt