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5.9 years ago
Shred
★
1.4k
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.
Is it
staxids
you are looking for?I'm looking for scientific names. I've tried using ssciname, but I still don't get the wanted results.