Question

Ncbi Standalone Blast -Outfmt

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11.3 years ago

bharat.85.monu ▴ 20

Hi,

I want to include the % of query coverage in my standalone blast result. Can anyone help me with this ??

Regards

BHARAT

blast • 7.0k views

ADD COMMENT • link updated 10.4 years ago by jacob18 ▴ 30 • written 11.3 years ago by bharat.85.monu ▴ 20

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Can you be more clear on what exactly you want to parse out from your BLAST? Query length, percent homology, or something else? When I hear "coverage" I am thinking assembly.

ADD REPLY • link 11.3 years ago by Josh Herr 5.8k

Ram · Answer 1 · 2013-12-07

3

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10.4 years ago

jacob18 ▴ 30

You need to include 'qcov' in the -outfmt argument. Here is an example:

-outfmt '10 qseqid sseqid stitle pident evalue qcovs'

Took me a while to figure this out too!

ADD COMMENT • link updated 4.3 years ago by Ram 43k • written 10.4 years ago by jacob18 ▴ 30

score 0 · Answer 2 · 2012-12-19

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11.3 years ago

lelle ▴ 830

Looking at the blast help for the tabular output it seems what you want is not implemented in blast. Only percentage values available are: "Percentage of identical matches" and "Percentage of positive-scoring matches". You will probably have to compute the value yourself.

ADD COMMENT • link 11.3 years ago by lelle ▴ 830