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

**URL:** <https://help.galaxyproject.org/t/best-galaxy-tools-workflow-to-analyze-scrnaseq-series-matrix-from-nih-geo/5344>\
**Category:** Uncategorized\
**Tags:** single-cell\
**Created:** [February 9, 2021, 12:09am UTC](https://help.galaxyproject.org/t/best-galaxy-tools-workflow-to-analyze-scrnaseq-series-matrix-from-nih-geo/5344 "2021-02-09T00:09:18Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![tshum](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/tshum/32/1924_2.png) [@tshum](https://help.galaxyproject.org/u/tshum)\
**Post date:** [February 9, 2021, 12:09am UTC](https://help.galaxyproject.org/t/best-galaxy-tools-workflow-to-analyze-scrnaseq-series-matrix-from-nih-geo/5344/1 "2021-02-09T00:09:19Z")

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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 [Shibboleth Authentication Request](https://science-sciencemag-org.ezp-prod1.hul.harvard.edu/content/352/6282/189). They have provided a series matrix at GEO “[GEO Accession viewer](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72056)”. 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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**Author:** ![mtekman](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/mtekman/32/752_2.png) [@mtekman](https://help.galaxyproject.org/u/mtekman)\
**Post date:** [February 9, 2021, 1:11pm UTC](https://help.galaxyproject.org/t/best-galaxy-tools-workflow-to-analyze-scrnaseq-series-matrix-from-nih-geo/5344/2 "2021-02-09T13:11:43Z")

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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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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [February 9, 2021, 6:35pm UTC](https://help.galaxyproject.org/t/best-galaxy-tools-workflow-to-analyze-scrnaseq-series-matrix-from-nih-geo/5344/3 "2021-02-09T18:35:30Z")

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GTN Tutorials: [Galaxy Training!](https://training.galaxyproject.org/training-material/search?query=scrna)

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**Author:** ![tshum](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/tshum/32/1924_2.png) [@tshum](https://help.galaxyproject.org/u/tshum)\
**Post date:** [February 9, 2021, 11:45pm UTC](https://help.galaxyproject.org/t/best-galaxy-tools-workflow-to-analyze-scrnaseq-series-matrix-from-nih-geo/5344/4 "2021-02-09T23:45:20Z")

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