Welcome, @nanohacker1
It looks like you used the reference genome (chromosomes) instead of the reference transcriptome (transcripts). I also do not see your reference annotation included for the Salmon step – you will usually want to include it for the gene-transcript mapping, at the Salmon step then later for DESeq2.
The best advice I have is to get all of your reference data organized at the very start. The UseGalaxy servers will host the genome indexed, but you’ll need to supply the two other files, and UCSC hosts all of this data.
We have discussions about this, so please have a review and let us know if you have any followup questions.
- Start here Correct reference transcriptome for Salmon quant on existing RNASTAR alignments - #2 by jennaj
- Then this post has an example where I loaded all the file choices from UCSC, reformatted, and tagged the “matched files”. Correct reference transcriptome for Salmon quant on existing RNASTAR alignments - #4 by jennaj
- Suggested data formatting for these tools. FAQ: Extended Help for Differential Expression Analysis Tools
- More is under reference-transcriptome and reference-genome and reference-annotation
- Human data has extra tips in this guide Reference genomes at public Galaxy servers: GRCh38/hg38 example
Hopefully this helps! 