scRNAseq: Count and Load with Cell Ranger
Version 1

Workflow Type: Galaxy
Stable

Takes fastqs and reference data, to produce a single cell counts matrix into and save in annData format - adding a column called sample with the sample name.

Inputs

ID Name Description Type
Fastqs for one sample Fastqs for one sample Typically the Forward reads are labelled _R1, barcodes. R2 is Reverse, mRNA sequences. List should contain seq for one biological sample only.
  • File[]
Reference genome Reference genome Built in reference dataset to use (human or mouse only)
  • string
Sample Sample Short, unique sample name
  • string

Steps

ID Name Description
3 Cell Ranger cellranger
4 Scanpy Read10x toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+1+galaxy0
5 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1
6 Create text file toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0
7 Text transformation This step replaces the first line with a header. Because the annotated data matrix also had a header, this works. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
8 Loaded Anndata with Sample name AnnData object with supplied sample id. toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1

Outputs

ID Name Description Type
AnnData Loaded AnnData Loaded n/a
  • File

Version History

main @ abc9384 (earliest) Created 9th Nov 2023 at 01:26 by Sarah Williams

now with cellranger pipelines


Frozen main abc9384
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
Other (Not Open)
Activity

Views: 899

Created: 9th Nov 2023 at 01:26

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Total size: 3.6 MB
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