GFF3 format from ucsc
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@sean-davis-490
Last seen 4 days ago
United States
Just wondering if anyone knew of code to take a ucsc Genome Browser tab-delimited file obtained via download and converting it to GFF3 format? Thanks, Sean
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Malcolm Cook ★ 1.6k
@malcolm-cook-6293
Last seen 6 weeks ago
United States
hmmm http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1088304 refers to psl2gff which can be found at http://lgsun.grc.nia.nih.gov/geneindex4/download.html -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sean Davis Sent: Monday, August 08, 2005 5:45 AM To: Bioconductor Subject: [BioC] GFF3 format from ucsc Just wondering if anyone knew of code to take a ucsc Genome Browser tab-delimited file obtained via download and converting it to GFF3 format? Thanks, Sean _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
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@sean-davis-490
Last seen 4 days ago
United States
Thanks, Malcolm. Looks good--I'll give it a whirl. Sean 1On 8/15/05 6:52 PM, "Cook, Malcolm" <mec at="" stowers-institute.org=""> wrote: > hmmm > > http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1088304 refers > to psl2gff which can be found at > http://lgsun.grc.nia.nih.gov/geneindex4/download.html > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sean Davis > Sent: Monday, August 08, 2005 5:45 AM > To: Bioconductor > Subject: [BioC] GFF3 format from ucsc > > > Just wondering if anyone knew of code to take a ucsc Genome Browser > tab-delimited file obtained via download and converting it to GFF3 > format? > > Thanks, > Sean > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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maximilianh ▴ 10
@maximilianh-11016
Last seen 7.3 years ago
UCSC

It depends on the format of your tab-sep file. If you have a genePred file, the only one where GFF really makes sense, UCSC has the tool genePredToGtf, and Gtf is just a somewhat tighter-spec GFF file .

The tool can be downloaded from http://hgdownload.soe.ucsc.edu/admin/exe/

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