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  • morning latte
    Member
    • Jun 2013
    • 91
    #1

    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!
    Tags: None
    • maubp
      Peter (Biopython etc)
      • Jul 2009
      • 1544
      #2
      BLAST+ tabular (and comma separated) output can be requested with columns for the coverage.

      I have some related examples here http://blastedbio.blogspot.co.uk/201...r-and-csv.html

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