Workflow Type: Galaxy
Open
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Associated Tutorial
This workflows is part of the tutorial Workflow 3: Functional Information, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Pratik Jagtap, Subina Mehta, Ray Sajulga, Bérénice Batut, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr
Workflow Author(s): Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep
Inputs
ID | Name | Description | Type |
---|---|---|---|
Interlaced non-rRNA reads | Interlaced non-rRNA reads | n/a |
|
Predicted taxon relative abundances | Predicted taxon relative abundances | n/a |
|
Steps
ID | Name | Description |
---|---|---|
2 | Cut | Cut1 |
3 | Metabolic assignation | toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.7+galaxy0 |
4 | Renormalize | toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.6.0+galaxy0 |
5 | Renormalize | toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.6.0+galaxy0 |
6 | Regroup | toolshed.g2.bx.psu.edu/repos/iuc/humann_regroup_table/humann_regroup_table/3.6.0+galaxy0 |
7 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 |
8 | Unpack pathway abundances | toolshed.g2.bx.psu.edu/repos/iuc/humann_unpack_pathways/humann_unpack_pathways/3.6.0+galaxy0 |
9 | Rename features | toolshed.g2.bx.psu.edu/repos/iuc/humann_rename_table/humann_rename_table/3.6.0+galaxy0 |
10 | Split a HUMAnN table | toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.6.0+galaxy0 |
11 | Combination of taxonomic and metabolic assignations for gene families | toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.2.0 |
12 | Select | Grep1 |
13 | Select | Grep1 |
14 | Select | Grep1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
_anonymous_output_1 | _anonymous_output_1 | n/a |
|
HUMAnN on input dataset(s): Pathways and their abundance | HUMAnN on input dataset(s): Pathways and their abundance | n/a |
|
HUMAnN on input dataset(s): Pathways and their coverage | HUMAnN on input dataset(s): Pathways and their coverage | n/a |
|
HUMAnN on input dataset(s): Log | HUMAnN on input dataset(s): Log | n/a |
|
HUMAnN on input dataset(s): Gene families and their abundance | HUMAnN on input dataset(s): Gene families and their abundance | n/a |
|
_anonymous_output_2 | _anonymous_output_2 | n/a |
|
_anonymous_output_3 | _anonymous_output_3 | 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 |
|
Split a HUMAnN table on input dataset(s): Unstratified table | Split a HUMAnN table on input dataset(s): Unstratified table | n/a |
|
Split a HUMAnN table on input dataset(s): Stratified table | Split a HUMAnN table on input dataset(s): Stratified table | n/a |
|
species abundances | Combine MetaPhlAn2 and HUMAnN2 outputs on input dataset(s): Gene family abundances related to genus/species abundances | n/a |
|
_anonymous_output_7 | _anonymous_output_7 | n/a |
|
_anonymous_output_8 | _anonymous_output_8 | n/a |
|
_anonymous_output_9 | _anonymous_output_9 | n/a |
|
Version History
1.0 (earliest) Created 25th Jun 2024 at 10:55 by Helena Rasche
Added/updated 4 files
Open
master
249c3b2
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Activity
Views: 344 Downloads: 96
Created: 25th Jun 2024 at 10:55
Last updated: 25th Jun 2024 at 10:55
Attributions
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