GTN - Preprocessing of 10X scRNA-seq data
4.0

Workflow Type: Galaxy

Associated Tutorial

This workflows is part of the tutorial Pre-processing of 10X Single-Cell RNA Datasets, available in the GTN

Features

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, Pavankumar Videm

Tutorial Contributor(s): Wendi Bacon, Björn Grüning, Donny Vrins, Saskia Hiltemann, Helena Rasche, Pavankumar Videm, Mehmet Tekman, Bérénice Batut, Hans-Rudolf Hotz, Cristóbal Gallardo

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
3M-february-2018.txt.gz 3M-february-2018.txt.gz n/a
  • File
Homo_sapiens.GRCh37.75.gtf Homo_sapiens.GRCh37.75.gtf n/a
  • File
Reference Genome Reference Genome n/a
  • string
subset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz subset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz n/a
  • File
subset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz subset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz n/a
  • File
subset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz subset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz n/a
  • File
subset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz subset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz n/a
  • File

Steps

ID Name Description
7 RNA STARSolo toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1
8 DropletUtils DefaultDrops toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2
9 DropletUtils RankBarcodes toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2
10 DropletUtils EmptyDrops toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2

Version History

4.0 (earliest) Created 2nd Jun 2025 at 10:58 by GTN Bot

Added/updated 4 files


Open master 05fd517
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Created: 2nd Jun 2025 at 10:58

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