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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 |
|---|---|---|---|
| QC controlled forward reads | #main/QC controlled forward reads | n/a |
|
| QC controlled reverse reads | #main/QC controlled reverse reads | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Taxonomic assignation | toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy0 |
| 3 | Cut | Cut1 |
| 4 | Krona pie chart | toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 |
| 5 | Export to GraPhlAn | toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.20+galaxy0 |
| 6 | Generation, personalization and annotation of tree | toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0 |
| 7 | Visualisation (GraPhlAn) | toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Export to GraPhlAn on input dataset(s): Annotation | #main/Export to GraPhlAn on input dataset(s): Annotation | n/a |
|
| Export to GraPhlAn on input dataset(s): Tree | #main/Export to GraPhlAn on input dataset(s): Tree | n/a |
|
| Generation, personalization and annotation of tree on input dataset(s): Tree in PhyloXML | #main/Generation, personalization and annotation of tree on input dataset(s): Tree in PhyloXML | n/a |
|
| GraPhlAn on input dataset(s): PNG | #main/GraPhlAn on input dataset(s): PNG | n/a |
|
| MetaPhlAn on input dataset(s): BIOM file | #main/MetaPhlAn on input dataset(s): BIOM file | n/a |
|
| MetaPhlAn on input dataset(s): Bowtie2 output | #main/MetaPhlAn on input dataset(s): Bowtie2 output | n/a |
|
| MetaPhlAn on input dataset(s): Predicted taxon relative abundances | #main/MetaPhlAn on input dataset(s): Predicted taxon relative abundances | n/a |
|
| MetaPhlAn on input dataset(s): SAM file | #main/MetaPhlAn on input dataset(s): SAM file | n/a |
|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
|
| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
Version History
master
Creators and Submitter
Views: 46 Downloads: 4 Runs: 0
Created: 2nd Jun 2025 at 10:53
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
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Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
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- Scalable: Galaxy can run ...
Teams: Galaxy Training Network
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
