I am running Salmon (as I usually do) on galaxy, and I want to get the quantification on the gene level.
Previously, there was an option to choose what type of file I’m uploading (GTF or transcript ID to gene ID), and then provide the file. This was recently changed and now it is supposedly automatically determined which file is provided - and it says either can be provided. When I run Salmon I get transcript quantification but not gene quantification (it is all zeros).
Does anyone know how to fix this? obviously something has changed in the platform but i am providing the same inputs however not getting an output.