Workflow 3: Functional Information
1.0

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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

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SEEK ID: https://workflowhub.eu/workflows/1456?version=1

Inputs

ID Name Description Type
Interlaced non-rRNA reads Interlaced non-rRNA reads n/a
  • File
Predicted taxon relative abundances Predicted taxon relative abundances n/a
  • File

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
  • File
HUMAnN on input dataset(s): Pathways and their abundance HUMAnN on input dataset(s): Pathways and their abundance n/a
  • File
HUMAnN on input dataset(s): Pathways and their coverage HUMAnN on input dataset(s): Pathways and their coverage n/a
  • File
HUMAnN on input dataset(s): Log HUMAnN on input dataset(s): Log n/a
  • File
HUMAnN on input dataset(s): Gene families and their abundance HUMAnN on input dataset(s): Gene families and their abundance 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
_anonymous_output_5 _anonymous_output_5 n/a
  • File
_anonymous_output_6 _anonymous_output_6 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
Split a HUMAnN table on input dataset(s): Stratified table Split a HUMAnN table on input dataset(s): Stratified table 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_7 _anonymous_output_7 n/a
  • File
_anonymous_output_8 _anonymous_output_8 n/a
  • File
_anonymous_output_9 _anonymous_output_9 n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:54 by GTN Bot

Added/updated 4 files


Open master 128ebcb
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
humann
HUMAnN2
License
MIT License
Activity

Views: 38   Downloads: 3   Runs: 0

Created: 2nd Jun 2025 at 10:54

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