Sorry for basic question. I wonder is there any options in blastall I can use in order to get output in the same format as we get it using blast online on the NCBI website?
Specifically, I want to get "Sequences producing significant alignments:" line that contains columns: Accession Description Max score Total score Query coverage E value Max ident
But using blastall from command line
e.g. blastall -p blastx -i input.fa -d /blast/db/nr -a 4 -b 5 -v 5 -e 1e-20 -o output.file
I get only Accession Description Score (bits) E value columns.
However, I want also to get Query coverage and Max ident columns.
I didn't find solution in the blastall manual. Perhaps, it depends on the parameter -m, but there are many options...
Thanks in advance!
UPD: -m 9 (tabular with comment lines (post-processed, sorted) view) produces almost what I want, but it gives only an Accession ID without description. And something like gi|66734174|gb|AAY53484.1| isn't very helpful.
Specifically, I want to get "Sequences producing significant alignments:" line that contains columns: Accession Description Max score Total score Query coverage E value Max ident
But using blastall from command line
e.g. blastall -p blastx -i input.fa -d /blast/db/nr -a 4 -b 5 -v 5 -e 1e-20 -o output.file
I get only Accession Description Score (bits) E value columns.
However, I want also to get Query coverage and Max ident columns.
I didn't find solution in the blastall manual. Perhaps, it depends on the parameter -m, but there are many options...
Thanks in advance!
UPD: -m 9 (tabular with comment lines (post-processed, sorted) view) produces almost what I want, but it gives only an Accession ID without description. And something like gi|66734174|gb|AAY53484.1| isn't very helpful.
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