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Old 04-05-2010, 08:32 PM   #18
Location: Ames, IA

Join Date: Nov 2008
Posts: 57

Originally Posted by lpachter View Post
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.
Dear L Pachter
Thank you very much for your reply thanks also to RCJ. I understand your point about probabilistically assigning reads to transcripts. I will get back to our statistical group about this. However the procedure suggested by RCJ and seconded by you has me a bit confused. I used to think that the algorithm that Cufflinks uses assigns reads based on probability and it will be different for each transcript and also vary according to genome location. So how can a mere multiplication of FPKM by transcript length and aligned sequences give us tag count per transcript? Am I missing something too obvious here?

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