I am trying to filter out mitochondrial-specific nanopore reads from whole genome reads using minimap2 and samtools view. In addition I want to retain reads with an alignment score of 5000 or more, following a methodology suggested on a paper. However I don't know what alignment score is and how to adjust it to 5000 to achieve this goal and at what stage. I would appreciate to have your thoughts. Also, I would believe alignment score is different from mapping quality? (samtools view -q) Thanks.
So far my commands go like this:
minimap2 -ax map-ont -t 24 mito_genome.fa nanopore_reads.fastq.gz > mito.sam
samtools view -F 4 mito.sam > mito_mapped.sam