How To Calculate Base-Level Read Coverage Of Each Transcript ?

Question

[biorepine]

Dear Biostars, I am trying to remove the transcripts that have less than 0.1 average base-level read coverage. But I am quiet confused with calculation part. Any comments or answers would be appreciated. What if I calculate coverage of reads overlapping a transcript and divide them number of reads by transcript length? Does it answer my question ? Thanx in advance!

[Ashutosh Pandey]

Average base-level read coverage for a transcript = (Total number of reads * length of the read)/ Length of the transcript.

Answer 1

[Adrian Pelin]

why don't you just use cufflinks to calculate FPKMs, then filter based on that?