> I made some changes to the cufflinks and tophat wrapper to pull gtf files > from an indexed loc file as opposed to from history. The diff’s are > attached. I made it an optional feature. Please let me know if this makes its > way into galaxy-central.
Ilya, This looks like a good start. A couple questions: (1) Do you have a sample GTF indices file similar to e.g. bowtie_indices.loc.sample ? (2) Would it be useful to provide GTF index files in Cuffcompare, Cuffdiff, and Tophat as well? Thanks, J.
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