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Old 07-14-2009, 08:28 PM   #1
Location: new orleans

Join Date: Jun 2009
Posts: 12
Default Where can I obtain GFF file for human?

I want to supply TopHat with a GFF3 file of gene annotation, the pipeline will report the relative expression of each in the sample.

Does anyone know where can I download the GFF file for human?
Or is there a simple way to convert some other formats (like GTF) into GFF format?

I have tried UCSC and other websites and still cannot find a good way to obtain the GFF format file. If anyone knows that, please tell me.
Your help would be really appreciated!

Last edited by iloveneworleans; 08-01-2009 at 08:11 AM.
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Old 07-20-2009, 12:27 PM   #2
Senior Member
Location: Boston area

Join Date: Nov 2007
Posts: 747

It looks like the GTF format you mention is a GFF variant (, so you should be able to convert.

Alternatively, the typical format for the tracks from the UCSC Genome Browser would appear to contain the relevant information, so it should be straightforward to use your favorite language (Perl/Python/Ruby/Java/C#/*) to write a converter
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Old 07-20-2009, 02:19 PM   #3
Location: Seattle, WA

Join Date: Mar 2009
Posts: 87

I have had success using this but it crashes and can be unreliable:

your best bet is using BioPerl.
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