Salmon transcripts are not aggregated to genes at all

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.


1 Like

Hi @Daniel10

This does sound buggy. I’d like to review and make a ticket to fix this if it can be confirmed.

You are working at Galaxy Main, correct? If yes, two ways to grant me access to the problematic results. Please do not delete any of the inputs/outputs.

  1. If your registered email address is the same as the one here, reply and state so. Also, include the name of the history and which dataset number(s) represent the poor results.

  2. If different, direct message me with your account email address at this server (no need to share it publically) and include the same info.

Either is fine. I’m an admin here and at If there is a bug, we want to squash it :bug: