Workflow 1: Preprocessing
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 Workflow 1: Preprocessing, 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

SEEK ID: https://dev.workflowhub.eu/workflows/1092?version=1

ID	Name	Description	Type
T1A_forward	T1A_forward	n/a	File
T1A_reverse	T1A_reverse	n/a	File

ID	Name	Description
2	Quality control Forward	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
3	Quality control Reverse	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
4	Cutadapt	toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1
5	MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
6	rRNA/rDNA selection	toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.6
7	FASTQ interlacer	toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0

ID	Name	Description	Type
FastQC on input dataset(s): RawData	FastQC on input dataset(s): RawData	n/a	File
FastQC on input dataset(s): Webpage	FastQC on input dataset(s): Webpage	n/a	File
_anonymous_output_1	_anonymous_output_1	n/a	File
_anonymous_output_2	_anonymous_output_2	n/a	File
Cutadapt on input dataset(s): Read 1 Output	Cutadapt on input dataset(s): Read 1 Output	n/a	File
_anonymous_output_3	_anonymous_output_3	n/a	File
Cutadapt on input dataset(s): Read 2 Output	Cutadapt on input dataset(s): Read 2 Output	n/a	File
MultiQC on input dataset(s): Stats	MultiQC on input dataset(s): Stats	n/a	File
MultiQC on input dataset(s): Webpage	MultiQC on input dataset(s): Webpage	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
_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
FASTQ interlacer singles from input dataset(s)	FASTQ interlacer singles from input dataset(s)	n/a	File
FASTQ interlacer pairs from input dataset(s)	FASTQ interlacer pairs from input dataset(s)	n/a	File