Thanks @hugo.avila works perfectly
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Hi Biostars,
I would like to get outputs with 100 percent identity and coverage in blastp. This is my command
blastp -task blastp-short -query infile.fa -db database.fa -out outfile.txt -outfmt 6
Thank you
It may exist an easiest way to do it, but here is how i do:
replace the last arg (-output) of your command by this:
-outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovs qcovhsp'
And then with some kind of text manning tool, filter by pident and qcov:
awk '$3 == 100 && $13 == 100 {print}' outfile.txt > filtered_outfile.txt
Be aware of multiple hits for the same query, choose the ones that have the best evalue and bitscore.
Thanks @hugo.avila works perfectly
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Do you want 100% identity and coverage (i.e. global search) or do you want to use BLAST (i.e. local search)?
Both will be fine, all I want is to get only protein hits that has 100 percent identity to the querry from the blastp
Ah, the classic or vs xor confusion - you cannot have both. Pick one.
Ok, I want to use blastp (i.e local search). Thanks