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Old 04-05-2010, 09:23 AM   #16
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Location: Rochester, MN

Join Date: Mar 2009
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Originally Posted by lpachter View Post
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.
Why not just take the FPKM values categorized by cufflinks for each individual transcripts and multiply them by transcript length and number of aligned sequences? That would give you the tag count per transcript.
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