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

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

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!

rna-seq coverage

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updated 12.7 years ago by Adrian Pelin

• written 12.7 years ago by biorepine

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

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written 12.7 years ago by Ashutosh Pandey

1 answer

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

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written 12.7 years ago by Adrian Pelin

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