I am Juan and I am very very new in this community. I am starting doing NGS data analysis and I have some doubts.
I using BWA to map my reads against a reference sequence. Afterwards I convert the sam file into a bam file that I can use to get a consensus sequence.My doubt is whether the sam/bam file I get after the mapping includes paired reads as well as the unpaired reads matching the reference sequence or only the paired reads and removes the reads as they don't have a mate.
Thanks in advance