Preprocessing of 10X scRNA-seq data
Visit source
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: 495 Downloads: 162
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
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service, Hu's Test
Web page: Not specified
Space: General
Public web page: https://galaxy.training
