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Old 09-19-2012, 03:43 AM   #2
Location: Iceland

Join Date: Apr 2012
Posts: 28

It is not unusual (I think) that many transcripts have an FPKM of value 0 - just means that that transcript is not expressed.

However if all transcripts have an FPKM value of 0 then something is wrong. My first guess would be that the chromosome names in the reference does not match the chromosome names in the annotation.
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