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Old 04-05-2010, 08:50 AM   #15
Location: Berkeley, cA

Join Date: Feb 2010
Posts: 40

Dear Siva,

I'd like to understand why your statistics collaborator cannot use the Cufflinks FPKM values together with their confidence intervals?

Regarding absolute counts, the whole point of Cufflinks is that it is not possible to obtain absolute read counts per transcript, because for many reads there is ambiguity as to which transcript they belong to. Cufflinks is probabilistically assigning reads to transcripts and thereby able to estimate expression of individual transcripts.
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