Homepage > Man Pages > Category > General Commands
Homepage > Man Pages > Name > U

ucsc_genes2gff.pl

man page of ucsc_genes2gff.pl

ucsc_genes2gff.pl: Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into gbrowse

NAME

ucsc_genes2gff.pl - Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into gbrowse

SYNOPSIS

% uscsc_genes2gff.pl [options] ucsc_file1 ucsc_file2... Options: -src <string> Choose a source for the gene, default "UCSC" -origin <integer> Choose a relative position to number from, default is "1"

DESCRIPTION

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
SEE ALSO
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
AUTHOR
Lincoln Stein <lstein@cshl.org>. Copyright (c) 2003 Cold Spring Harbor Laboratory This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty. UCSC_GENES2GFF.PL(1)
 
 
 

Copyright © 2011–2018 by topics-of-interest.com . All rights reserved. Hosted by all-inkl.
Contact · Imprint · Privacy

Page generated in 51.64ms.

fliegender-drache.de | get-ip.de | generiere.de