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Old 01-04-2011, 05:17 AM   #1
Location: beijing, china

Join Date: Jun 2010
Posts: 36
Default questions for cuffcompare and cuffdiff output

After I run cuffcompare, there is a prefix.loci file which is not explained in the user manual. I guess it is the combined gene file for different samples. However, after I run cuffdiff, the items in cuffdiff output genes.fpkm_tracking are much less than the items in prefix.loci. Why so many "gene" outputed by cuffcompare discarded by cuffdiff?
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