Entering edit mode
3.2 years ago
Mgs3
▴
30
I'm using blastx version 2.2.27+ and the subsequent command
blastx -db nr -query fasta -outfmt '6 qseqid sgi sacc sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore stitle' -evalue 1e-10 -num_alignments 1 -num_threads 24 -out blast_farm_50_20.txt
that give me this output:
ERR1017187.18398 gi|319772954|gb|ADV73297.1| 100.00 50 0 0 2 151 76 125 6e-25 104
ERR1017187.23471 gi|1401185531|gb|PYV37130.1| 92.00 50 4 0 1 150 373 422 8e-22 97.4
Which contain every information that i need except the description of the match, below is the output of the default blastx (in bold the part that i need)
ref|WP_133160687.1| **hypothetical protein [Candidatus Sulfotelmat..**. 97.4 2e-22
gb|PYX33850.1| **hydrophobe/amphiphile efflux-1 family RND transpo...** 94.0 7e-20
what i need to add to the first command to obtain the description?
Have you tried moving
stitle
to beginning of your specification for format 6? Aftersacc
perhaps.Unfortunately it doesn't work