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
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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!
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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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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.