Workflow Type: Galaxy
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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 |
---|---|---|---|
Barcode Whitelist file | #main/Barcode Whitelist file | Obtain from kit supplier e.g. 10X |
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Expected Cells | #main/Expected Cells | Approximately how many cells are expected in this sample? |
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Paired Fastqs for one sample | #main/Paired 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. |
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Reference Genome fasta | #main/Reference Genome fasta | n/a |
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Reference annotation | #main/Reference annotation | n/a |
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Sample | #main/Sample | Short, unique sample name |
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Steps
ID | Name | Description |
---|---|---|
6 | Unzip collection | __UNZIP_COLLECTION__ |
7 | Forward/R1/barcode Fastq Concat | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
8 | Reverse/R2/mRNA Fastq concat | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
9 | RNA STARSolo | toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0 |
10 | Scanpy Read10x | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.9.3+galaxy0 |
11 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 |
12 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1 |
13 | 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 |
14 | 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 | #main/AnnData Loaded | n/a |
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RNA STARSolo on input dataset(s): Alignments | #main/RNA STARSolo on input dataset(s): Alignments | n/a |
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Feature Statistic Summaries | #main/RNA STARSolo on input dataset(s): Barcode/Feature Statistic Summaries | n/a |
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RNA STARSolo on input dataset(s): Barcodes filtered | #main/RNA STARSolo on input dataset(s): Barcodes filtered | n/a |
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RNA STARSolo on input dataset(s): Genes filtered | #main/RNA STARSolo on input dataset(s): Genes filtered | n/a |
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RNA STARSolo on input dataset(s): Matrix Gene Counts filtered | #main/RNA STARSolo on input dataset(s): Matrix Gene Counts filtered | n/a |
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RNA STARSolo on input dataset(s): log | #main/RNA STARSolo on input dataset(s): log | n/a |
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Version History
main @ 7581788 (latest) Created 30th May 2024 at 06:47 by Sarah Williams
Updated workflow versions for anndata version conflict bugfix
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main
7581788
main @ fe052c0 Created 12th Dec 2023 at 03:08 by Sarah Williams
updated star solo index size to limit RAM useage since galaxy migration
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main
fe052c0
main @ a95a4ee (earliest) Created 22nd Jun 2023 at 07:47 by Sarah Williams
counts matrix workflow doc, affiliations
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main
a95a4ee
Creators and Submitter
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Citation
Williams, S., Thang, M., & Murigneaux, V. (2023). {scRNAseq on galaxy workflows}.
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Views: 4413 Downloads: 437 Runs: 0
Created: 22nd Jun 2023 at 07:47
Last updated: 30th May 2024 at 06:47
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