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Old 06-20-2013, 08:47 AM   #1
dekkers
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Location: MN

Join Date: Jun 2013
Posts: 4
Default Gene id using cufflink and cuffdiff with UCSC table as reference

Hi,
I'm new to the world of RNA seq and have run into an issue using the UCSC table (directly from Galaxy) for annotation (equine). When I get my cufflink and cuffdiff data at the end, it has gene ids in a format that I can't seem to transfer to gene name. Example: CD468286

Has anybody used this as the gtf file and gotten back gene names that made sense? When I look at the mapped tophat data in igv it shows that the refseq data has correct identifiers.

Thanks for any help!
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