bed2gff31p

Usage

Overview

This script massages the gene files available from the "tables" link of the UCSC genome browser (genome.ucsc.edu) into a form suitable for loading of gbrowse. Warning: it only works with the gene tables. Other tables, such as EST alignments, contours and repeats, have their own formats which will require other scripts to parse.

To use this script, get one or more UCSC tables, either from the "Tables" link on the browser, or from the UCSC Genome Browser FTP site. Give the table file as the argument to this script. You may want to provide an alternative "source" field. Otherwise this script defaults to "UCSC".

  % pucsc_genes2gff.pl -src RefSeq refseq_data.ucsc > refseq.gff

The resulting GFF file can then be loaded into a Bio::DB::GFF database using the following command:

  % bulk_load_gff.pl -d <databasename> refseq.gff