Was able to track down that the input for mirtop is basically seqcluster collapsed reads (trimmed reads that have collapsed and then re-mapped back to the full genome.) Is this summary correct: reads are trimmed/UMIs removed --> mapped with seqbuster, collapsed with seqcluster --> aligned to genome --> this bam is input to mirtop?

trying to figure this out as well

Hi Tyler, was able to figure out that the trimmed reads are collapsed with seqcluster and then these collapsed reads are aligned directly to the hairpin sequences)

@Michael Martinez Do you know the logic of aligning to hairpin index as opposed to mature miRNA index?