Workflow 3: Functional Information (quick)
1.0

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

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

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
Gene Family abundance Gene Family abundance n/a
  • File
Pathway abundance Pathway abundance n/a
  • File
Predicted taxon relative abundances Predicted taxon relative abundances n/a
  • File

Steps

ID Name Description
3 Cut Cut1
4 Renormalize toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.7+galaxy0
5 Regroup toolshed.g2.bx.psu.edu/repos/iuc/humann_regroup_table/humann_regroup_table/3.7+galaxy0
6 Renormalize toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.7+galaxy0
7 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
8 Rename features toolshed.g2.bx.psu.edu/repos/iuc/humann_rename_table/humann_rename_table/3.7+galaxy0
9 Split a HUMAnN table toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.7+galaxy0
10 Unpack pathway abundances toolshed.g2.bx.psu.edu/repos/iuc/humann_unpack_pathways/humann_unpack_pathways/3.7+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
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File
_anonymous_output_3 _anonymous_output_3 n/a
  • File
_anonymous_output_4 _anonymous_output_4 n/a
  • File
Split a HUMAnN table on input dataset(s): Stratified table Split a HUMAnN table on input dataset(s): Stratified table n/a
  • File
Split a HUMAnN table on input dataset(s): Unstratified table Split a HUMAnN table on input dataset(s): Unstratified table n/a
  • File
_anonymous_output_5 _anonymous_output_5 n/a
  • File
species abundances Combine MetaPhlAn2 and HUMAnN2 outputs on input dataset(s): Gene family abundances related to genus/species abundances n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File
_anonymous_output_7 _anonymous_output_7 n/a
  • File
_anonymous_output_8 _anonymous_output_8 n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:53 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 10:53

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