I'm working on RNA-seq on BAM file (single read) containing as optional fields the NH and HI tags, used to make featureCounts analisys. For example i have NH:i:6 and 1<=HI<=6.
From https://samtools.github.io/hts-specs/SAMtags.pdf the tag definitions are:
NH:i:count Number of reported alignments that contain the query in the current record. HI:i:i Query hit index, indicating the alignment record is the i-th one stored in SAM.
In case of paired-end reads with multiple alignments, I have a doubt on how these tags work?
read1 has 4 alignments read2 has 7 alignments
So i I'll see NH:i:4 for read1 and NH:i:7 for read2, or one NH:i:11 (7+4). The same with HI, i'll see 1<=HI<=4 for read1 and 1<=HI<=7 for read2, or one 1<=HI<=11 (7+4)?