Workflow Type: Galaxy
Frozen
Frozen
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. |
|
Reference genome | Reference genome | Built in reference dataset to use (human or mouse only) |
|
Sample | Sample | Short, unique sample name |
|
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/1.9.3+galaxy0 |
5 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 |
6 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1 |
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/9.3+galaxy1 |
8 | Loaded Anndata with Sample name | AnnData object with supplied sample id. toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
AnnData Loaded | AnnData Loaded | n/a |
|
Version History
main @ 7581788 (latest) Created 30th May 2024 at 06:49 by Sarah Williams
Updated workflow versions for anndata version conflict bugfix
Frozen
main
7581788
main @ abc9384 (earliest) Created 9th Nov 2023 at 01:26 by Sarah Williams
now with cellranger pipelines
Frozen
main
abc9384
Creators and Submitter
Creators
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Citation
Williams, S., Thang, M., & Murigneaux, V. (2023). {scRNAseq on galaxy workflows}.
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Views: 3753 Downloads: 287 Runs: 0
Created: 9th Nov 2023 at 01:26
Last updated: 30th May 2024 at 06:56
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