TopHat GFF

[seq_GA]

Hi,

Where can I download GFF file for human and mouse knowngene list or how do I convert from knowngene downloaded from UCSC to GFF3 format? thanks.

[choy]

http://www.sequenceontology.org has a good GTF to GFF3 converter that you can use.

You can download GTF's from UCSC genome browser.

[seq_GA]

Thanks for the info.

[scozza]

I believe though that the converter at that site has a warning about the UCSC GTF output causing issues because of the identifiers it uses. I haven't looked at it in a while though and perhaps that has changed.

[RockChalkJayhawk]

I believe though that the converter at that site has a warning about the UCSC GTF output causing issues because of the identifiers it uses. I haven't looked at it in a while though and perhaps that has changed.

But you can fix the identifies so the transcripts never have the same name as the gene. For example:

perl -ane '@F[11]=~s/";$/_a";/g;print"@F\n"' hg19.RefFlat.GTF

Do you know what the config file for the Seq ontology converter is?