We are looking into the possibility of off-target mapping for some sequences that were added to our alignment reference. We are only concerned about off-target mapping to genes (including introns). We are also only concerned about off-target mapping in mouse.
To look at this I want to do a blast search on ~1000 sequences that mapped to our added sequence, only to the mouse genome and only to genes (including introns). I have a fasta file for mm10 and a gtf file describing the genes, but I am unsure how to put this into blast + (blast CLI) so that I know that I am searching genes.