Annotation of Deseq2 results not giving full results

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Hi @mfaleevs

I think I saw you ask this in another topic but I can’t find it again. That’s Ok.

How to solve most reference annotation problems:

  1. Make sure to use the same exact reference annotation for all steps in the same analysis.
  2. That could be a built-in annotation (only supported with a few tools, and for a few reference genomes) or an annotation supplied by you from the history.
  3. GTF formatted annotation tends to work best. UCSC has this for hg38. Be sure to get it from their Downloads area, and not from the Table Browser. I’ll add a tag that links to prior Q&A with the “why”, or you can just try this way instead :slight_smile:
  4. See the last section in this FAQ for exactly where to source the data and how to get it into Galaxy → Working with GFF GFT GTF2 GFF3 reference annotation
  5. Once the file is in your history, toggle the tool from to use “annotation from the history” and select the dataset.