Workflow Type: Galaxy
Metatranscriptomics 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 |
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QC controlled reverse reads | #main/QC controlled reverse reads | n/a |
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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 |
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Export to GraPhlAn on input dataset(s): Tree | #main/Export to GraPhlAn on input dataset(s): Tree | n/a |
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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 |
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GraPhlAn on input dataset(s): PNG | #main/GraPhlAn on input dataset(s): PNG | n/a |
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MetaPhlAn on input dataset(s): BIOM file | #main/MetaPhlAn on input dataset(s): BIOM file | n/a |
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MetaPhlAn on input dataset(s): Bowtie2 output | #main/MetaPhlAn on input dataset(s): Bowtie2 output | n/a |
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MetaPhlAn on input dataset(s): Predicted taxon relative abundances | #main/MetaPhlAn on input dataset(s): Predicted taxon relative abundances | n/a |
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MetaPhlAn on input dataset(s): SAM file | #main/MetaPhlAn on input dataset(s): SAM file | n/a |
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_anonymous_output_1 | #main/_anonymous_output_1 | n/a |
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_anonymous_output_2 | #main/_anonymous_output_2 | n/a |
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_anonymous_output_3 | #main/_anonymous_output_3 | n/a |
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_anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
Version History

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Created: 2nd Jun 2025 at 10:53

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