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

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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?
Thanks
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Old 06-02-2009, 11:12 AM   #2
geriatrics1200
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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: http://www.sequenceontology.org/reso...databases.html
and please let me know if it works.

If anybody knows where to find the same file for mouse, please let me know
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Old 06-15-2009, 12:46 AM   #3
warrenemmett
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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
http://bcbio.wordpress.com/2009/03/2...sing-and-gff2/

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 !!!

Warren
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