Dear Experts, I use Htsat2 output file for running feature-counts, but when I set up the run Galaxy doesn't t recognize Rat annotation file in history(Rattus_norvegicus.Rnor_6.0.92.gtf, which I uploaded) what am I doing wrong?
First, the tool form option Gene annotation file should be set to "in your history". GTF datasets will appear in the select menu.
The database metadata assignment should be the same between all inputs. Also, the datatype metadata assignments must be made to all. It is very important that the genome build/version is the same for all inputs/steps (have content with respect to the same "database") or tool errors will result.
- My job ended with an error. What can I do?
- Common datatypes explained
- The tool I'm using does not recognize any input datasets. Why? << Try this first
- How do I find, adjust, and/or correct metadata?
- Mismatched Chromosome identifiers (and how to avoid them) << Make sure the genome mapped against is a match for your annotation, or find another source that is. iGenomes is one choice for
rn6UCSC based annotation: https://support.illumina.com/sequencing/sequencing_software/igenome.html. Download the tar archive locally, uncompress it, and upload just the
genes.gtffile to Galaxy.
Thanks! Jen, Galaxy team