I'm trying to map nanopore reads to a mtDNA reference using minimap2 for the purpose of determining how many mitochondrial reads are present in the nanopore data.
The minimap command I'm using is;
~/apps/minimap2/minimap2 -ax map-ont mtref.fa reads.fq > aln.sam
I know there are mtDNA reads present as I can align them to the reference, however when I look at the resulting indexed and sorted sam file in IGV there's no coverage?
Thanks!
Have you made a custom genome in IGV using the same reference? By default IGV shows you the entire reference so you may need to zoom in before you start seeing the reads.
I have. I solved the initial problem by actually creating a sorted bam file and using that in IGV rather than just the same file. Thanks!