Question: Showing the original subject when running BLAST
gravatar for kdsilva
4.3 years ago by
kdsilva0 wrote:

I'm running the following command:

blastn -query references.fasta -subject reads.fasta -task blastn-short -outfmt "6" -out output.csv

I would like to see the ENTIRE subject sequence in the output. Is there a way to do this? It looks like including "sseq" in the outfmt shows me the aligned part of the subject sequence, but I'd like to see the entire thing.

dna blast alignment read command • 983 views
ADD COMMENTlink modified 20 months ago by RamRS27k • written 4.3 years ago by kdsilva0

You can always look-up the entire sequence using the subject identifier. BLAST is local alignment, it doesn't concern itself with entire sequences.

ADD REPLYlink written 4.3 years ago by RamRS27k
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: 1716 users visited in the last hour