After FeatureCounts, gene name disappears

I am using the following for the differential expression of my samples.

  1. HISAT2
  2. StringTie
  3. StringMerge
  4. GffCompare
  5. FeatureCount

Gene names are still in the file until GffCompare. However, after FeatureCount, all the gene names disappear leaving only the ensembl ID and stringtie ID. Can anyone help me troubleshoot it? Thank you so much. My history is shared below.

Hi @Josh

Only the value that is annotated as the “gene_id” will be populated in the downstream outputs.

What to do

  1. Use a tool like AnnotateMyIDs to pull in public alternative names for your current values. Scroll down to the bottom of the tool form to find the tutorials that include it to view how it is usually incorporated.

  2. Convert your GFF to a tabular format (gffread) then use one of the join tools to merge in the data that you want in a final output file. More about data manipulation tools → Hands-on: Data Manipulation Olympics / Introduction to Galaxy Analyses

Hope this helps! You can ask more questions if this was not enough. :slight_smile: