Assigning multi-gene classes

[Jesse Niehaus]

Hi Alex,

Thanks again for the tool!
Quick question:
Is it possible to incorporate one class of multi-gene multimapped reads and not another?

In the starSolo paper you describe two classes of multi-gene reads:
1. Read aligns to a single genomic coordinate where multiple genes overlap
2. Read aligns to multiple genomic coordinates containing genes

I would like to employ the EM algorithm on reads that apply to scenario 1, but discard reads in scenario 2. Is there a parameter that could facilitate this?
I'm working w/ 10x scRNA-seq data if that matters.

Cheers,
Jesse

[Alexander Dobin]

Hi Jesse,

Presently there is no way to separate these classes.