Gene-level data from oarfish outputs

[lianov]

Hello oarfish team,

First, thank you for developing oarfish. We are close to a new release of nf-core/scnanoseq where oarfish will be added as a quantifier (the pipeline processes single-cell data from Oxford sequencing). But one follow-up question (for another future release), is to also provide users with gene-level matrices from oarfish data since by default it produces transcripts only.

I just checked a few other issues/discussions here, and noted that oarfish support was added to tximport (https://github.com/thelovelab/tximeta/issues/81) - would this be (in your opinion), the best approach to summarize oarfish's transcripts to genes much like Salmon's? (I have not yet tested tximport implementation of oarfish - thought I would check here first in case there were other thoughts)

Edited for context: unsure if the nature of the request is clear or not - but a main driver to this data is to have gene-level as a comparison data point to isoform expression (in analysis from IsoQuant outputs, it's helpful to have both gene and transcript quantifications). Happy to expand on this if needed.

Thanks