Hi @SehajR
I have a copy of the completed protocol in this shared history. Maybe comparing to these steps helps? → https://usegalaxy.eu/u/jenj/h/gtn-differential-isoform-expression-1
XREF tutorial → Hands-on: Genome-wide alternative splicing analysis / Genome-wide alternative splicing analysis / Transcriptomics
Then, for your first error, I would be curious about what the Job Details view looks like for this job. Find this using the i-info icon. The tool is reporting that there is a duplication in one of the inputs. That is just a guess by the tool – so there could be a repeated input file but also inspect that view in general. Example: toggle open the inputs and check to make sure these all have the expected content, and are not empty.
And for the second error, yes, the issue has to do with a mismatch with the reference data. The input data for the tutorial includes a special downsampled set of reference files. You’ll want to use those. Or, you can replace these with full reference versions. But a hybrid approach is not likely to work well – and most of those “mismatched data” errors will look like yours. One of the annotation files (GFF files) includes a sequence that was not in the genome fasta files. Maybe one genome was used for upstream steps, and a different one for downstream steps? Instead, using the same assembly version throughout an analysis is usually required.
Bonus guide about reference data → Reference genomes at public Galaxy servers: GRCh38/hg38 example
Please let us know if this helps, and if you would like more help, you are welcome to share back your history!