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Old 05-26-2009, 05:28 PM   #1
Location: ca

Join Date: Feb 2008
Posts: 39
Default GFF file for TopHat

I am analyzing mRNA-Seq generated by solexa from human samples; I would like to run TopHat with a GFF file in order to obtain gene expression values (-G option).
Can any body point out where can I get a GFF file for human genome?
joseph is offline   Reply With Quote
Old 06-02-2009, 11:12 AM   #2
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Location: boston, ma

Join Date: Jun 2009
Posts: 3

I've been looking for the same file but for mouse.

I did come across such files being available for many organisms (including human but not mouse). Try this:
and please let me know if it works.

If anybody knows where to find the same file for mouse, please let me know
geriatrics1200 is offline   Reply With Quote
Old 06-15-2009, 12:46 AM   #3
Location: South Africa

Join Date: Nov 2008
Posts: 23

Hi there,

How I did it, although there is definitely a better way. I downloaded the UCSC knowngene table for human in BED format and converted it to GFF2 (through GALAXY). I then converted that to GFF3 using the package on this site

As I said there is definitely a better way to do this, I only needed to convert a single file so I never looked any further. However if anyone knows of a straight BED to GFF3 converter (or a package that can convert between other annotation file formats) please post it !!!

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