Best Galaxy tools/workflow to analyze scRNAseq Series Matrix from NIH GEO?

Hi everyone,

I’m trying to replicate the results of the scRNAseq dataset from the following publication “Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq” from this link https://science-sciencemag-org.ezp-prod1.hul.harvard.edu/content/352/6282/189. They have provided a series matrix at GEO “GEO Accession viewer”. I would like advice from the forum on the best Galaxy tools to format this file for analysis.

I thought this file looked like a a processed dataset (like what we would get after RNA-Star Solo pre-processing), so I started out by putting this directly into the RACEID Initial Processing to make a Count Matrix (RDS). However this didn’t work. When I tried to plug this directly into the RACEID clustering directly, I also got an error.

What are the proper steps and tools to process a series matrix into a matrix I can put it into RACEID for analysis? Thanks for your help!

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Hello,

Please try with ScanPy instead. RaceID is great on smaller datasets but struggles a bit on larger ones.

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GTN Tutorials: Galaxy Training!

Thanks, I will go with Scanpy then and do the training for it. Appreciate the help!

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