Question: Display full information about taxa instead of staxids in BLASTn
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gravatar for Shred
12 months ago by
Shred150
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 • 339 views
ADD COMMENTlink written 12 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 12 months ago • written 12 months ago by h.mon24k

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

ADD REPLYlink written 12 months ago by Shred150
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