Question: Display full information about taxa instead of staxids in BLASTn
gravatar for Shred
17 months ago by
Shred150 wrote:

Hi guys, I'm new at using BLAST locally from command line. I'm trying to find a way to display the full taxonomy information instead of staxid in Blastn output. Here's the command using till today:

$ blastn -query contigs.fasta -db BacteriaDB -evalue 10 -outfmt "7 qseqid qlen slen qcovhsp sseqid stax evalue score" -num_alignments 10 -out output.txt

The idea here is to get the output (I'm telling always as a taxonomy level) as provided by the standard "3" for outfmt

$ blastn -query contigs.fasta -db BacteriaDB -outfmt 3

Even some crispy tool to easly convert this code into the full name of taxid will be appreciated. Thanks.

blast genomic taxonomy • 478 views
ADD COMMENTlink written 17 months ago by Shred150
    staxid means Subject Taxonomy ID

   staxids means unique Subject Taxonomy ID(s), separated by a ';'
         (in numerical order)

Is it staxids you are looking for?

ADD REPLYlink modified 17 months ago • written 17 months ago by h.mon27k

I'm looking for scientific names. I've tried using ssciname, but I still don't get the wanted results.

ADD REPLYlink written 17 months ago by Shred150
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2169 users visited in the last hour