Question: Looping local blastn in bash
2.8 years ago by
maximilian.mayerhofer • 30 wrote:
I have a Folder containing multiple genomes as .fasta files.
strainA.fasta strainB.fasta strainC.fasta ....
I have set up a local blast db called "dbGOI.fasta"
I want to blast all the genomes against my local db.
for file in dir do blastn -in *.fasta -db dbGOI.fasta -out blast[strainname].txt done
But as you might guess, it does not work as intended.
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