Reference annotation file (gtf) for the NOD/ShiltJ mouse?

[michelletran]

Hi,

I am in desperately looking for a reference annotation file (gtf) for the NOD/ShiltJ mouse so that I may run Cuffmerge.

I cannot find one in gtf format. Help would be very, very, very much appreciated!

Thanks,

Michelle

[dpryan]

Did you align against the de novo assembled genome? I don't think there are annotations for those.

[michelletran]

How would I go about doing RNA-seq processing using Galaxy? How can I get any idea about the names of genes without an annotation file?

[dpryan]

How you go about things depends entirely on the circumstances and goals.

I suppose you could blast things. If you really want to not use the standard mouse reference, then it would be much easier to use something like modmap with the VCF file for that species to create more or less appropriate GTF and fasta files and then use those with cufflinks/cuffdiff/cuffmerge.

I haven't a clue if that's possible in Galaxy, I've never looked.