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Forum: Bioinformatics 11-15-2010, 10:30 AM
Replies: 0
Views: 1,707
Posted By burkard
cuffdiff not strand-specific?

Hi,

regardless which --library-type I specify, I get always the same FPKM results with cuffdiff. Contrary cufflinks seems to give strand specific results. All cuffdiff FPKMs correlate best with...
Forum: Bioinformatics 08-05-2010, 11:52 PM
Replies: 0
Views: 3,385
Posted By burkard
DESeq: Read counts vs. BP counts

Hi Simon,

is it possible to use raw bp counts (how often a bp is sequenced within a region) of an exon/transcript for differential expression analysis with DESeq?
First I think, that if we...
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