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 Workflow 3: Functional Information (quick), available in the GTN

Features

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

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 25th Jun 2024 at 10:55 by Helena Rasche

Added/updated 4 files


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Views: 308   Downloads: 81

Created: 25th Jun 2024 at 10:55

Last updated: 25th Jun 2024 at 10:55

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