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Old 08-23-2015, 10:36 AM   #1
morning latte
Location: MI

Join Date: Jun 2013
Posts: 91
Default BLAST out - query coverage

Hello experts,

I have blast output which contains score, e-value, identities, and positives information. I think it is called standard blast. I am wondering if there is any way (by using command) to extract query coverage information from this output file. If I need to run BLAST again with an additional flag to get query coverage information, please let me know. Or maybe I should run BLAST with -m flag and get alignment length and calculate query coverage from there?

Any advice would be greatly appreciated!
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Old 08-23-2015, 12:37 PM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542

BLAST+ tabular (and comma separated) output can be requested with columns for the coverage.

I have some related examples here
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