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Old 04-23-2012, 04:16 PM   #4
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Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 438

Seems like a very strange error. I've never had to resort GTF files in order to get them to work with Cufflinks/merge/diff. I'm surprised the GTF files is giving you this kind of trouble.

I almost always use GTF files from UCSC that I edit in the official gene names to make the DE output more readable. Aside from swapping in gene names I don't change anything. I'm also working with bowtie references I built from FASTA files downloaded from UCSC.
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