Workflow 1: Preprocessing 1.0
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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
Thanks to...
Workflow Author(s): Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, 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): Bérénice Batut, Helena Rasche, Saskia Hiltemann, Paul Zierep
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| T1A_forward | T1A_forward | n/a |
|
| T1A_reverse | T1A_reverse | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Quality control Forward | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 3 | Quality control Reverse | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 4 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1 |
| 5 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
| 6 | rRNA/rDNA selection | toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.6 |
| 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 on input dataset(s): RawData | FastQC on input dataset(s): RawData | n/a |
|
| FastQC on input dataset(s): Webpage | FastQC on input dataset(s): Webpage | n/a |
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| _anonymous_output_1 | _anonymous_output_1 | n/a |
|
| _anonymous_output_2 | _anonymous_output_2 | n/a |
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| Cutadapt on input dataset(s): Read 1 Output | Cutadapt on input dataset(s): Read 1 Output | n/a |
|
| _anonymous_output_3 | _anonymous_output_3 | n/a |
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| Cutadapt on input dataset(s): Read 2 Output | Cutadapt on input dataset(s): Read 2 Output | n/a |
|
| MultiQC on input dataset(s): Stats | MultiQC on input dataset(s): Stats | n/a |
|
| MultiQC on input dataset(s): Webpage | MultiQC on input dataset(s): Webpage | n/a |
|
| _anonymous_output_4 | _anonymous_output_4 | n/a |
|
| _anonymous_output_5 | _anonymous_output_5 | n/a |
|
| _anonymous_output_6 | _anonymous_output_6 | n/a |
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| _anonymous_output_7 | _anonymous_output_7 | n/a |
|
| _anonymous_output_8 | _anonymous_output_8 | n/a |
|
| _anonymous_output_9 | _anonymous_output_9 | n/a |
|
| FASTQ interlacer singles from input dataset(s) | FASTQ interlacer singles from input dataset(s) | n/a |
|
| FASTQ interlacer pairs from input dataset(s) | FASTQ interlacer pairs from input dataset(s) | n/a |
|
Version History
master
Creators and Submitter
Views: 39 Downloads: 4 Runs: 0
Created: 2nd Jun 2025 at 10:53
AttributionsNone
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Teams: Galaxy Training Network
Organizations: Galaxy
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