Single-cell analysis-Seurat not working

usegalaxy.org support
1

Hi all!

I have two things, one, I can’t get Seurat to work despite inputting the correct files (or at least I think I’m putting it in correctly). Additionally, I have gene names that I would prefer to have in my ‘feature’ files but it just giving me the accession (further into the workflow) as it’s in the first column.

Susan

2

Welcome, @lichenlady94

You can covert the gene labels with the tool AnnotateMyIDs. But maybe do that last, during graphing steps, or you might introduce problems.

Single-cell protocols can be found at our training site.

Topic Category: https://training.galaxyproject.org/training-material/topics/single-cell/

Learning Pathway: https://training.galaxyproject.org/training-material/learning-pathways/

And, for single-cell data, there are some upstream steps to reduce the overall matrix size, before doing any actual analysis. If that part is skipped, most tools will die, in Galaxy or otherwise. Maybe review the tutorials and see if that wasn’t done yet?

Once you think things are Ok, and you still have some error, you can post back your data and errors for more specific help. How to:

:mechanic: What information should I include when reporting a problem?

Any persistent problems can be reported in a new question for community help. Be sure to provide enough context so others can review the situation exactly and quickly offer advice.

Consider Sharing your History or posting content from the Job Information :information_source: view as described in Troubleshooting errors.