Workflow 3: Functional Information

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

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	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