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Ncbi Standalone Blast -Outfmt

Hi,

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

Regards

BHARAT

blast

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.

2 answers

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!

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.

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