Error Running StringTie with HISAT2 and annotated File

Hello Everyone,

I am having issues running StringTie in Galaxy. When I run StringTie, I input my aligned reads from HISAT2 and my annotated GTF file. However, after running I receive the following error codes:

  1. Fatal error: Exit code 1 ()
  2. Error: no valid ID found for GFF record

Does anyone know what the issue could be?

Hi @tgray4
The error message points on data incompatibility. Maybe check the contig/chromosome names in the reference genome and annotation file. The names should be identical. Note that chr1 and 1 are different names.
Hope that helps.
If not, please share the history, so people can check what is going on.
Kind regards,

1 Like

XRef FAQ: Extended Help for Differential Expression Analysis Tools