Question: Re: Rna Seq Analysis And Gtf Files
7.7 years ago by
Jeremy Goecks • 2.2k
Jeremy Goecks • 2.2k wrote:
Slim, Please send questions to the galaxy-user mailing list (cc'd) rather than individual Galaxy team members; there are many people on the list that may be able to address your question, and discussions are archived for future use as well. Without seeing your analysis, I'd suggest trying two things: (1) Provide gene annotation reference file to Cufflinks as well as Cuffcompare and Cuffdiff; in other words, you'll want to do guided assembly. (2) Try using an Ensembl GTF, which has the gene name in the attributes. I think (2) is more likely to generate the results you want, but there are the many known problems in using Ensembl GTFs with Cufflinks/compare/diff. Good luck, J.
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