mRNA-Seq BY-COVID Pipeline: Counts 1.0
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Run on GalaxyThis portion of the workflow produces sets of feature Counts ready for analysis by limma/etc.
Associated Tutorial
This workflows is part of the tutorial Pathway analysis with the MINERVA Platform, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Iacopo Cristoferi, Helena Rasche, Clinical Bioinformatics Unit, Pathology Department, Eramus Medical Center
Tutorial Author(s): Marek Ostaszewski, Matti Hoch, Iacopo Cristoferi, Myrthe van Baardwijk, Saskia Hiltemann, Helena Rasche
Tutorial Contributor(s): Helena Rasche, Matti Hoch, Mira Kuntz, José Manuel Domínguez, Sanjay Kumar Srikakulam, Björn Grüning, Linelle Abueg, Saskia Hiltemann
Grants(s): BeYond-COVID
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| UCSC Genome | #main/UCSC Genome | Export of UCSC Genome, just the genes. |
|
| mRNA-Seq Reads | #main/mRNA-Seq Reads | Input list of fastqsanger format sequencing data |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 |
| 3 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0 |
| 4 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 |
| 5 | HISAT2 | toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1 |
| 6 | featureCounts | toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy1 |
| 7 | Read Distribution | toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.1+galaxy2 |
| 8 | Gene Body Coverage (BAM) | toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.1+galaxy2 |
| 9 | Multi QC raw reads | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| html_report | #main/html_report | n/a |
|
| output_feature_lengths | #main/output_feature_lengths | n/a |
|
| output_short | #main/output_short | n/a |
|
Version History
master
Creators and Submitter
Views: 1131 Downloads: 175 Runs: 0
Created: 2nd Jun 2025 at 11:03
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