Hi all, I am working with makeblastdb and blastn for the first time and apologize for what is probably a basic question. I recently indexed and blasted against my own database, all of which are the sequences from the same species.
module load BLAST+/2.9.0-foss-2018a blastn -query my.fasta -db my_databse -out -evalue 0.0001 -num_threads 4
I am now interested in counting the number of hits in my samples that match the sequences in my blast database. Any advice on the best methods to do this would be fantastic! Thanks in advance for any help. Cheers