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Old 04-10-2011, 02:59 PM   #1
ega2d
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Location: Virginia

Join Date: Oct 2010
Posts: 12
Question Isoform tracking in Cufflinks

Hi all,

I am using Cufflinks to look at differential expression of alternative splicing. The big problem that I'm running into is that when I go to visualize my data in IGV, I can't find the isoforms that Cufflinks has identified as "significant". In particular, I can't validate/confirm a single intron retention event as identified by the "i" class code, which you would think would be relatively easy, right?

Has anyone ever come up with a good way of tracking down the "significant" isoforms identified by Cufflinks?

Any help/advice/comments would be greatly appreciated!
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