Hi all, I already have taken a few suggestions on my data and making a custom reference from particular genomic locations and Suggestions worked great. Now when I am mapping my ONT reads to this custom reference I am getting like 10 to 15% reads mapped to it. I understand that mapping stats would probably go lower as now there are no off target regions in custom reference but my reads are amplified for those custom locations so percentage should not be this bad. I used minimap2 and bwa mem with different settings but it didn’t work. If I do get better alignment with changed parameters then mapping quality becomes really worse .
I tried bbmap too but same result. Can someone please suggest me alignment tools or settings which would work better with custom reference and ONT MinION reads? p.s- I have some locations in custom reference which are like1 or 2 bp long( in case this is contributing in poor alignment?)
