9 months ago by
It looks like you are using the GTF version based on hg38. The version of the annotation that is based on hg19 is here: https://www.gencodegenes.org/releases/27lift37.html
Two choices (both assume that you obtained valid hits with HISAT2):
- Map against hg38 with HISAT2 instead
- Use the hg19 version of the GTF
Please try one of these and let us know if you still have problems. If working at https://usegalaxy.org, an email with a history share link to your working history can be sent to email@example.com for closer review. Please leave all inputs and outputs undeleted.
The server at https://usegalaxy.org is undergoing updates right now and several tools are undergoing adjustments. I am not aware of this tool being problematic and would expect a different failure if your results were related to the other known issues, but we can check (after the mismatch issue with the annotation versus genome version is corrected).
Thanks! Jen, Galaxy team