Is any way to retrieve the read counts per transcript instead of per gene to detect isoform expression?

Recount is a great tool, thank you very much for creating it!

Hi,

This is currently not possible with recount3, though it's been considered at https://github.com/LieberInstitute/recount3/issues/18.

For the recount2 project (recount package), we do have estimated transcript quantifications. See this preprint by Fu et al, 2018 https://www.biorxiv.org/content/10.1101/247346v2. See recount::download_study(type = "rse-tx") at http://leekgroup.github.io/recount/reference/download_study.html for more details.

Best, Leo