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Old 09-15-2015, 06:16 AM   #4
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

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.
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