Does what it says on the tin! As of Salmon version 1.5.0, the --tgMap option is not needed with --rad, so I removed it from the alevin workflow.
These version updates add much more informative output files for all stages of the workflow. Notably, though, the output file from alevin quant changes from meta_info.json to quant.json, which will require changes to scpcaTools (tracked in https://github.com/AlexsLemonade/scpcaTools/issues/24)
Does what it says on the tin! As of Salmon version 1.5.0, the
--tgMapoption is not needed with--rad, so I removed it from the alevin workflow.These version updates add much more informative output files for all stages of the workflow. Notably, though, the output file from
alevin quantchanges frommeta_info.jsontoquant.json, which will require changes to scpcaTools (tracked in https://github.com/AlexsLemonade/scpcaTools/issues/24)Closes #118