Workflow 3: Functional Information
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, 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
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 25th Jun 2024 at 10:55 by Helena Rasche

Added/updated 4 files


Open master 249c3b2
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Views: 344   Downloads: 96

Created: 25th Jun 2024 at 10:55

Last updated: 25th Jun 2024 at 10:55

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