I would like to count the number of reads aligning per viruses in my sample based on the output of minimap2 in a bam file.
Does anyone how to proceed?
By using the command:
samtools view -f 2 ech22ReadsViralSorted.bam, I am able to see the alignments, but I am unsure about how to process the file.
Attached is the link to download the sample ech22ReadsViralSorted.bam