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?
1 answer
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.
Log in to answer this question.
-
Difference between perc_identity and qcov_hsp_perc in blastn
written by 090d5b56 •
-
BLAST output
written by torquato.f.o •
-
How to run Blastn on an input data with manual database?
written by mthm •
-
Puzzling NCBI BLAST+ output after transcriptome assembly
written by ella •
-
Blast command line gives no hits
written by Vca80553 •
-
How to filter BLAST results by query coverage? How to analyze large BLAST outputs?
written by braun_tube •
-
Blast locally on multiple fasta files with multiple database
written by fec2 •
-
Blastn error, database creation problem, BLAST
written by biomagician
-
blastn query coverage filter
written by fortwatts •
-
Blast - Formatting Output
written by timjoncooper
Do not delete posts that have received feedback. Your post has an accepted answer, and deleting it takes away from the forum's value.