Preprocessing of 10X scRNA-seq data
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Download RO-CrateAssociated Tutorial
This workflows is part of the tutorial Pre-processing of 10X Single-Cell RNA Datasets, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Wendi Bacon, Pavankumar Videm, Mehmet Tekman, Hans-Rudolf Hotz, Daniel Blankenberg
Tutorial Author(s): Mehmet Tekman, Hans-Rudolf Hotz, Daniel Blankenberg, Wendi Bacon, Pavankumar Videm
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| 3M-february-2018.txt.gz | 3M-february-2018.txt.gz | n/a |
|
| Homo_sapiens.GRCh37.75.gtf | Homo_sapiens.GRCh37.75.gtf | n/a |
|
| subset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz | subset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz | n/a |
|
| subset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz | subset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz | n/a |
|
| subset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz | subset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz | n/a |
|
| subset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz | subset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 6 | RNA STARSolo | toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy3 |
| 7 | DropletUtils | toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 |
| 8 | DropletUtils | toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 |
| 9 | DropletUtils | toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 |
Version History
2.0 (latest) Created 7th Oct 2024 at 14:09 by Helena Rasche
Added/updated 4 files
Open
master5dd16a9
3.0 (earliest) Created 25th Jun 2024 at 11:12 by Helena Rasche
Added/updated 4 files
Frozen
3.09700704
Creators and Submitter
Views: 751 Downloads: 246
Created: 25th Jun 2024 at 11:12
Last updated: 7th Oct 2024 at 14:09
AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
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