Workflow Type: Galaxy
Stable

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


Frozen main fe052c0

main @ 03682c0 Created 9th Nov 2023 at 01:58 by Sarah Williams

some differences in single sample workflows updated


Frozen main 03682c0

main @ a95a4ee Created 22nd Jun 2023 at 07:36 by Sarah Williams

counts matrix workflow doc, affiliations


Frozen main a95a4ee

master @ 76f52ed (earliest) Created 5th May 2023 at 07:29 by Sarah Williams

count and load


Frozen master 76f52ed
help Creators and Submitter
Creators
  • Sarah Williams
  • Mike Thang
  • Valentine Murigneaux
Submitter
Citation
Williams, S., Thang, M., & Murigneaux, V. (2023). {scRNAseq on galaxy workflows}.
License
Activity

Views: 4559   Downloads: 614   Runs: 0

Created: 5th May 2023 at 07:29

Last updated: 30th May 2024 at 06:54

help Tags
help Attributions

None

Total size: 3.6 MB
Powered by
(v.1.16.0-main)
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH