blastn: how to show all query list in my blastn results, even if they have no match.

Question

[nuria.mauri]

Hi,

I am comparing a list of sequences from my sequencing results with public database and saving just the best record like this:

blastn -task blastn -query ${i}.fa -db nt -remote -outfmt '6 qseqid sseqid pident evalue staxids stitle' -num_alignments 1 -out ${i}_blastnxnt.csv

But, I would like to have one line per query line, saving all ids, even those not found in the database. Does anyone know how to do it?

Gracias!

Answer 1

[Sej Modha]

Showing Queries With No Hit In Tabbed Blast Output?

[nuria.mauri]

That's it, with a value for the whole query list.

Answer 2

[Chirag Parsania]

Before you move ahead to find find one best hit, I would strongly suggest you to read recently published paper talking about finding best hit and its misunderstanding

[lakhujanivijay]

+1 for that Chirag..!