Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 1: Preprocessing
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Run on GalaxyMetatranscriptomics analysis using microbiome RNA-seq data (short)
Associated Tutorial
This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
- Uses Galaxy Workflow Comments
Thanks to...
Workflow Author(s): Bérénice Batut, Pratik Jagtap, Subina Mehta, Saskia Hiltemann, Paul Zierep
Tutorial Author(s): Pratik Jagtap, Subina Mehta, Ray Sajulga, Bérénice Batut, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr
Tutorial Contributor(s): Christine Oger, Bérénice Batut, Helena Rasche, Saskia Hiltemann, Paul Zierep, Björn Grüning
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Forward raw reads | Forward raw reads | Metatranscriptomics forward raw reads |
|
| Reverse raw reads | Reverse raw reads | Metatranscriptomics reverse raw reads |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 |
| 3 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 |
| 4 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0 |
| 5 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 |
| 6 | Filter with SortMeRNA | toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/4.3.6+galaxy0 |
| 7 | FASTQ interlacer | toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| fastqc_reverse_html_file | fastqc_reverse_html_file | n/a |
|
| fastqc_forward_html_file | fastqc_forward_html_file | n/a |
|
| cutadapt_report | cutadapt_report | n/a |
|
| multiqc_html_report | multiqc_html_report | n/a |
|
| sortmerna_unaligned_reverse | sortmerna_unaligned_reverse | n/a |
|
| sortmerna_unaligned_forward | sortmerna_unaligned_forward | n/a |
|
Version History
master
1.0
Creators and Submitter
Views: 218 Downloads: 32 Runs: 0
Created: 2nd Jun 2025 at 10:53
Last updated: 23rd Jun 2025 at 14:13
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Organizations: Galaxy
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