how to have aligned region in fasta format using blastn?

Question

[mthm]

I want to blast my genome against a manual database:

 blastn -db ref-database.fa -query genome.fa -perc_identity 80  -qcov_hsp_perc 80 -out result.out

to have the hits as a fasta alignment, but non of my output files are in sequence alignment format, how should I do that?

[Ram]

Do not delete posts that have received feedback. Your post has an accepted answer, and deleting it takes away from the forum's value.

Answer 1

[GenoMax]

You are using a couple of different terminologies in this post so I will address them separately.

how to have aligned region in fasta format using blastn

You will need to extract the fasta sequences of hits from your blast database using blastdbcmd and then align the sequences. See: https://www.ncbi.nlm.nih.gov/books/NBK279689/

but non of my output files are in sequence alignment format,

SAM format is used for reporting alignments from NGS data. If that is what you are looking for then you will have to use magicblast (LINK) which is a variant of blast meant for NGS data.