Entering edit mode
2.5 years ago
setschmann
▴
10
Hi, I'm visualizing a genome, and i have to be able to get from a blast search result to the location of the hit.
So im running a BLAST instance locally, and I already generated a BLAST db. Searching against this db works, but i don't know where the hits are. I would need to know in what fasta file the sequence was found to visualize it in jbrowse.
any ideas?
Your blast results should include chromosome designation of the hits and their coordinates. What is the specific use case of need to visualize? If you are starting with fastq reads you could look at using
magicblast
(LINK) which can create BAM files for visualization.i have a reference genome with a lot of contigs, so the contigs where it was found should be somewhere in the blast results? so heres an example of a result
If you have a blast "hit" then the hit record should always contain the accession/name of the reference for the
subject
. Yourquery
may show multiple hits (and multiple HSPs on the same hit as well).In example above:
okay thank you, now how do cross reference that? is there a way to get the location in the original fasta file i used for creating the db?
Edit: okay I think I forgot to -parse_seqid when generating the db, that's why I can't find anything lol