Apologies that I don't have a lot of experience with this stuff, but It's been a long time since I am struggling with this issue.
I am aligning my RNA seq data of a heterologous gene library from nanopore to the reference database, and I am getting such mismatches.
I have verified my reference database, there is no problem with that, I think some of the genes are misaligning with others. I wanted your suggestions on what parameters can I set with the minimap2 aligning command so these mismatches disappear. Currently, my command line looks like this:
minimap2 -ax map-ont reference.fasta rna_seq.fastq > output.sam
After this, I also filter the alignments to keep only primary ones (FLAG 0 & 16) with a mapping quality of at least 10 (MAPQ10).
I would really appreciate your help. Thanks