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Old 10-18-2011, 05:46 AM   #1
hezichia
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Location: Athens. GA

Join Date: Oct 2011
Posts: 1
Default Get query coverage using CLI blast

I'm running blastall locally but can not find an option to include query coverage in the output. How do I add query coverage to the blastall output?

I would even be happy with query length in the output as query coverage would then be easily calculated using alignment length.

This problem seems to be addressed in this thread: http://seqanswers.com/forums/showthread.php?t=9971 however I was unable to find a query length output option in blast_formatter.

Thanks.
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Old 03-05-2013, 10:41 PM   #2
lzsph
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Default

I haven't used blastall before, I just used NCBI BLAST+ 2.2.26.
For example, with the local blastx tool.

Code:
$blastx -db db_name -query input_file -out output -evalue evalue -outfmt "6 qlen" -num_threads 4
Only 6, 7, and 10 option of
Code:
-outfmt
allows you add additional column. If you want to add extra column(s), delimited using space ,such as
Code:
"6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen"
The first 12 columns are default columns, you can also delete it. The last qlen is what you want to add.

You can dind the detailed documentation http://computing.bio.cam.ac.uk/local/doc/blast+_user_manual.pdf in section 4.2.26 outfmt.

Last edited by lzsph; 03-05-2013 at 11:18 PM.
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blast, blastall, blast_fromatter, query coverage

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