Workflow Type: Galaxy
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From the R1 and R2 fastq files of a single samples, make a scRNAseq counts matrix, and perform basic QC with scanpy. Then, do further processing by making a UMAP and clustering. Produces a processed AnnData
Depreciated: use individual workflows insead for multiple samples
Steps
ID | Name | Description |
---|---|---|
10 | scRNAseq: Count and Load with starSOLO | n/a |
11 | scRNAseq_CellQC | n/a |
12 | scRNAseq_QCtoBasicProcessing | n/a |
Version History
main @ fe052c0 (latest) Created 12th Dec 2023 at 03:15 by Sarah Williams
updated star solo index size to limit RAM useage since galaxy migration
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main
fe052c0
main @ 03682c0 Created 9th Nov 2023 at 01:58 by Sarah Williams
some differences in single sample workflows updated
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main
03682c0
main @ a95a4ee Created 22nd Jun 2023 at 07:36 by Sarah Williams
counts matrix workflow doc, affiliations
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a95a4ee
master @ 76f52ed (earliest) Created 5th May 2023 at 07:29 by Sarah Williams
count and load
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master
76f52ed
Creators and Submitter
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Citation
Williams, S., Thang, M., & Murigneaux, V. (2023). {scRNAseq on galaxy workflows}.
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Views: 4559 Downloads: 614 Runs: 0
Created: 5th May 2023 at 07:29
Last updated: 30th May 2024 at 06:54
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