I have some Fastq files of the mouse(later mapped to the B6=mm10 reference sequence).
But when I looked at bam files with IGV, some reads were found out to be Rat's (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001895.5)
I have used web Blastn to check some of the reads but it is impossible to check all the reads one by one.
I installed Blastn for Linux but I couldn't figure out how to use it for comparing with limited reference sequences (In my case, I want to compare the reads with only mouse and rat reference sequences)
If you could help me, I would be grateful.