I have several primer pairs and want to map them onto genome, then calculate the coverage.
My plan now is as follows:
using BSgenome to load the genome library;
using function matchPattern in BSgenome to get the start and end information of the primer pairs;
using function getseq to get sequences;
alignment these sequences with genome sequence and calculate the coverage.
I'm wondering is there a packages which can map the primer pair on genome and get the sequences directly?
Thanks in advance!