Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 1: Preprocessing

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, 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): Christine Oger, Bérénice Batut, Helena Rasche, Saskia Hiltemann, Paul Zierep, Björn Grüning

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
Forward raw reads Forward raw reads Metatranscriptomics forward raw reads
  • File
Reverse raw reads Reverse raw reads Metatranscriptomics reverse raw reads
  • File

Steps

ID Name Description
2 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
3 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
4 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0
5 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3
6 Filter with SortMeRNA toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/4.3.6+galaxy0
7 FASTQ interlacer toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0

Outputs

ID Name Description Type
fastqc_reverse_html_file fastqc_reverse_html_file n/a
  • File
fastqc_forward_html_file fastqc_forward_html_file n/a
  • File
cutadapt_report cutadapt_report n/a
  • File
multiqc_html_report multiqc_html_report n/a
  • File
sortmerna_unaligned_reverse sortmerna_unaligned_reverse n/a
  • File
sortmerna_unaligned_forward sortmerna_unaligned_forward n/a
  • File

Version History

2.0 (latest) Created 23rd Jun 2025 at 14:13 by GTN Bot

Added/updated 4 files


Open master 70c991b

1.0 (earliest) Created 2nd Jun 2025 at 10:53 by GTN Bot

Added/updated 4 files


Frozen 1.0 7f672fa
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Created: 2nd Jun 2025 at 10:53

Last updated: 23rd Jun 2025 at 14:13

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