[New Feature Request] --transcript-count for counting

[akmazian]

[update]: oops, I just realized you can use kallisto quant-tcc to do this

I know there are workarounds for this but it would be nice to have a --transcript-counts option for bustools count that acts similar as --genecounts :)

Rationale:

• for certain purposes, e.g. when studying transcript isoforms, collapsing everything to gene-level loses useful information

Current workaround:

• create a t2t.txt file that maps each transcript to itself and use it in place of t2g.txt

[Yenaled]

yup, just get your TCC matrix (omit --genecounts and put --multimapping to allow reads mapped to multiple genes to be preserved) and then run quant-tcc on the resulting matrix. This is basically the same as running kallisto for bulk RNA-seq (which gets you isoform-level quantification in an accurate probabilistic manner).