I have used minimap2 to map some pacbio reads to a reference genome. I would like to know the "insert size" (true length of sequence) relative to the reference. More specifically, I want to know the first base position in the reference where the read maps and the last base position in the reference where the mapping ends.
As I understand it I need the TLEN field from bam files (sam format field 9). However, all the alignment files from minimap2 have 0
in the TLEN field.
Does anyone know how to get pacbio alignments with the TLEN field? I am also happy using bwa
or another aligner.
The command I used was minimap2 -ax map-pb {fasta} {reads} | samtools view -h -b - | samtools sort - > myfile.bam
.