I am studying a repetitive region in which multiple lncRNAs are transcribed. For now, I am following the HISAT2-StringTie pipeline to assemble and quantify novel lncRNAs from this region. Because of the repetitive nature of this region, I only want to keep reads that are
- not strictly uniquely mapped because there would be very few aligned reads left; and
- assigned to their best possible locations.
This is the default behavior for aligners like bowtie2 (in the manual, "Default mode: search for multiple alignments, report the best one"), but I did not find the options to do so in HISAT2 (in the manual, "Default mode: search for one or more alignments, report each"). The closet thing that I can find is to set
-k to 1, but that does not guarantee that the alignment is the BEST. I also cannot filter alignments based on their MAPQs, because there are only three MAPQ values available:
- 0 (unmapped)
- 1 (not uniquely mapped); and
- 60 (uniquely mapped).
Does anyone has experience to identify the best alignment using HISAT2? Thanks!