Hi, I am confused about the first line in cuffdiff (using Galaxy on the cloud, not sure if it's different for local instances). It reads:
Transcripts:(choose a file)A transcript GTF file produced by cufflinks, cuffcompare, or other source. What file should I load here? I have 4 groups of 2-4 replicates each that I am comparing, and am using the "grouping" option that follows. Should I use one of the files produced by cufflinks? If so, which ones? Or should I rather use the GTF file of RefSeq genes from the UCSC database? Thx!!A
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