Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 3: Functional Information
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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 |
|---|---|---|---|
| Interleaced reads | Interleaced reads | Metatranscriptomics interleaced reads |
|
| Taxonomic profile | Taxonomic profile | Taxonomic profile generated by MetaPhlAn |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | HUMAnN | toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.9+galaxy0 |
| 3 | Split a HUMAnN table | toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.9+galaxy0 |
| 4 | Regroup | toolshed.g2.bx.psu.edu/repos/iuc/humann_regroup_table/humann_regroup_table/3.9+galaxy0 |
| 5 | Renormalize | toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.9+galaxy0 |
| 6 | Rename features | toolshed.g2.bx.psu.edu/repos/iuc/humann_rename_table/humann_rename_table/3.9+galaxy0 |
| 7 | Renormalize | toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.9+galaxy0 |
| 8 | Split a HUMAnN table | toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.9+galaxy0 |
| 9 | Split a HUMAnN table | toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.9+galaxy0 |
| 10 | Rename features | toolshed.g2.bx.psu.edu/repos/iuc/humann_rename_table/humann_rename_table/3.9+galaxy0 |
| 11 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2 |
| 12 | Unpack pathway abundances | toolshed.g2.bx.psu.edu/repos/iuc/humann_unpack_pathways/humann_unpack_pathways/3.9+galaxy0 |
| 13 | Select | Grep1 |
| 14 | Select | Grep1 |
| 15 | Select | Grep1 |
| 16 | Split a HUMAnN table | toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.9+galaxy0 |
| 17 | Split a HUMAnN table | toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.9+galaxy0 |
| 18 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy2 |
| 19 | Split a HUMAnN table | toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.9+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| humann_gene_families | humann_gene_families | n/a |
|
| humann_pathabundance | humann_pathabundance | n/a |
|
| renormalize_gene_families | renormalize_gene_families | n/a |
|
| renormalize_pathabundance | renormalize_pathabundance | n/a |
|
| unpack_pathway_abundance | unpack_pathway_abundance | n/a |
|
| cc_go | cc_go | n/a |
|
| bp_go | bp_go | n/a |
|
| sorted_mf_go | sorted_mf_go | n/a |
|
Version History
master
1.0
Creators and Submitter
Views: 224 Downloads: 28 Runs: 0
Created: 2nd Jun 2025 at 10:54
Last updated: 23rd Jun 2025 at 14:13
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