Hello Team,
I am performing Refernce based RNA-Seq analysis, and I am stuck at the RNA STAR-based mapping step. After running with the following parameters, an error shows: An error occurred with this dataset. I am not sure how to troubleshoot.
Did you try a rerun already? If not, please try to see what happens.
Then, if this is reproducible, I would be curious if the full logs have more details. Find these on your Job Information Details page for the red error output.
If there is some issue with the annotation, you can try a different file to see what happens. UCSC is a good place to source! RefSeq is updated the quickest but all of the choices are described in the main browser and are useful for different reasons, so you can review. Each will be based on the GRCm38/mm10 genome assembly (also what is hosted in Galaxy, and what you already selected).
UCSC annotation
* Find annotation under their Downloads area. The path will be similar to:
`https://hgdownload.soe.ucsc.edu/goldenPath/<database>/bigZips/genes/`
* Copy the URL from UCSC and paste it into the Upload tool,
allowing Galaxy to detect the datatype.
That location would be in here. Be sure to get the mm10 data and not mm38! → https://hgdownload.gi.ucsc.edu/downloads.html#mouse
My guess is that there is either a formatting issue in the current annotation (header lines with # at the top) or the chromosome naming scheme is based on Ensembl format (1, 2, … X) and not UCSC format (chr1, chr2,.. chrX) or both! RNA-Star is very picky! The UCSC file will have both of these addressed already. Just capture the file link at UCSC, paste it into the Upload tool, use all defaults, and load it into your history and it’ll be ready to use.
Then, if that works, you can compare the formats between the two, if you want to use the other data for a specific purpose, to learn what you need to adjust in the original annotation to allow RNA Star to use it. We have a lot of discussion about this at the forum under reference-annotation but you can also ask! We would need to see the content of the file to help with this.
More about how different assembly versions can influence analysis choices is discussed here (all have similar considerations, not just human!) → Reference genomes at public Galaxy servers: GRCh38/hg38 example
Please let us know what happens!! 
I uploaded the gtf file from a different source, as you directed. Thanks it worked.
Great! Thanks for letting us know! 