Bin reads by mapping to transcriptome

[kbseah]

Like MILCOR but with transcriptome as reference instead, e.g. for use case where no reference genome is available.

Distinguish introns from IESs by GT/AG boundaries, and 100% "retention" of introns (vs. IESs, if the library is only an enrichment).

However splicing may result in erroneous indel calls; for minimap2 mapper, "splice" mode is not suitable for our needs because it assumes RNAseq reads are being mapped onto genomic reference, not the other way around. What we could do is to compare predicted intron positions on different isoforms, if available.