Workflow Type: Galaxy
Open
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
Inputs
ID | Name | Description | Type |
---|---|---|---|
Barcodes (single-col) | #main/Barcodes (single-col) | n/a |
|
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 |
|
_anonymous_output_11 | #main/_anonymous_output_11 | n/a |
|
_anonymous_output_12 | #main/_anonymous_output_12 | n/a |
|
_anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
_anonymous_output_5 | #main/_anonymous_output_5 | n/a |
|
_anonymous_output_6 | #main/_anonymous_output_6 | n/a |
|
_anonymous_output_7 | #main/_anonymous_output_7 | n/a |
|
_anonymous_output_8 | #main/_anonymous_output_8 | n/a |
|
_anonymous_output_9 | #main/_anonymous_output_9 | n/a |
|
Version History
1.0 (earliest) Created 25th Jun 2024 at 11:11 by Helena Rasche
Added/updated 4 files
Open
master
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Views: 132 Downloads: 50
Created: 25th Jun 2024 at 11:11
Last updated: 25th Jun 2024 at 11:11
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
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