CelSeq2: Single Batch (mm10)
1.0

Visit source Download RO-Crate
Workflow Type: Galaxy

Pre-processing of Single-Cell RNA Data

Associated Tutorial

This workflows is part of the tutorial CelSeq2: Single Batch (mm10), available in the GTN

Thanks to...

Tutorial Author(s): Mehmet Tekman, Bérénice Batut, Anika Erxleben, Wolfgang Maier

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1214?version=1

Inputs

ID Name Description Type
Barcodes (single-col) #main/Barcodes (single-col) n/a
  • File
Batch #main/Batch n/a
  • array containing
    • File
GTF file (UCSC) #main/GTF file (UCSC) n/a
  • File

Steps

ID Name Description
3 UMI-tools extract toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2
4 Alignment (Choose a Genome) The genome should match that of the GTF file toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2
5 Filter toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1
6 featureCounts toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2
7 UMI-tools count toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2

Outputs

ID Name Description Type
_anonymous_output_10 #main/_anonymous_output_10 n/a
  • File
_anonymous_output_11 #main/_anonymous_output_11 n/a
  • File
_anonymous_output_12 #main/_anonymous_output_12 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File
_anonymous_output_6 #main/_anonymous_output_6 n/a
  • File
_anonymous_output_7 #main/_anonymous_output_7 n/a
  • File
_anonymous_output_8 #main/_anonymous_output_8 n/a
  • File
_anonymous_output_9 #main/_anonymous_output_9 n/a
  • File

Version History

1.0 (earliest) Created 25th Jun 2024 at 11:11 by Helena Rasche

Added/updated 4 files


Open master 96c774a
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
UMI-tools
STAR
BamTools
FeatureCounts
License
Creative Commons Attribution 4.0 International
Activity

Views: 423   Downloads: 111

Created: 25th Jun 2024 at 11:11

Last updated: 25th Jun 2024 at 11:11

help Attributions

None

Total size: 69.3 KB
Powered by
 (v.1.16.0-main)
About Dev WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH