CelSeq2: Single Batch (mm10) 1.0
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Run on GalaxyPre-processing of Single-Cell RNA Data
Associated Tutorial
This workflows is part of the tutorial Pre-processing of Single-Cell RNA Data, available in the GTN
Thanks to...
Tutorial Author(s): Mehmet Tekman, Bérénice Batut, Anika Erxleben, Wolfgang Maier
Tutorial Contributor(s): Helena Rasche, Nicola Soranzo, Bérénice Batut, Björn Grüning, Mehmet Tekman, Saskia Hiltemann, Gildas Le Corguillé, Stéphanie Robin, Anthony Bretaudeau, Simon Bray, Wendi Bacon, Martin Čech, Armin Dadras
Funder(s): de.NBI
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Barcodes (single-col) | #main/Barcodes (single-col) | n/a |
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| Batch | #main/Batch | n/a |
|
| GTF file (UCSC) | #main/GTF file (UCSC) | n/a |
|
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 |
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| _anonymous_output_11 | #main/_anonymous_output_11 | n/a |
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| _anonymous_output_12 | #main/_anonymous_output_12 | n/a |
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| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
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| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
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| _anonymous_output_6 | #main/_anonymous_output_6 | n/a |
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| _anonymous_output_7 | #main/_anonymous_output_7 | n/a |
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| _anonymous_output_8 | #main/_anonymous_output_8 | n/a |
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| _anonymous_output_9 | #main/_anonymous_output_9 | n/a |
|
Version History
master
Creators and Submitter
Views: 220 Downloads: 30 Runs: 0
Created: 2nd Jun 2025 at 10:55
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