QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN

Reference-based RNA-Seq data analysis

Associated Tutorial

This workflows is part of the tutorial Reference-based RNA-Seq data analysis, available in the GTN

Features

Includes Galaxy Workflow Tests
Uses subworkflows

Thanks to...

Workflow Author(s): Bérénice Batut, Mallory Freeberg, Mo Heydarian, Anika Erxleben, Pavankumar Videm, Clemens Blank, Maria Doyle, Nicola Soranzo, Peter van Heusden, Lucille Delisle

Tutorial Author(s): Bérénice Batut, Mallory Freeberg, Mo Heydarian, Anika Erxleben, Pavankumar Videm, Clemens Blank, Maria Doyle, Nicola Soranzo, Peter van Heusden, Lucille Delisle

Tutorial Contributor(s): Helena Rasche, Clea Siguret, Wolfgang Maier, Pavankumar Videm, Bérénice Batut, Lucille Delisle, Björn Grüning, Nicola Soranzo, Hans-Rudolf Hotz, Cristóbal Gallardo, Saskia Hiltemann, Graeme Tyson, Maria Doyle, Amirhossein Naghsh Nilchi, Mehmet Tekman, Anika Erxleben, Simon Bray, Clemens Blank, Ekaterina Polkh, William Durand, Marius van den Beek, Niall Beard, Martin Čech, Armin Dadras

Funder(s): de.NBI

Inputs

ID	Name	Description	Type
Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz	Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz	gtf with genes	File
Paired list collection with PE fastqs	Paired list collection with PE fastqs	input fastqs	File[]

Steps

ID	Name	Description
2	Falco/MultiQC	n/a
3	cutadapt	n/a
4	STAR + multiQC	n/a
5	more QC	n/a
6	Determine strandness	n/a
7	count STAR	n/a
8	count featureCount	n/a

Outputs

ID	Name	Description	Type
multiqc_falco_html	multiqc_falco_html	n/a	File
multiqc_cutadapt_html	multiqc_cutadapt_html	n/a	File
multiqc_star_html	multiqc_star_html	n/a	File
STAR_BAM	STAR_BAM	n/a	File
multiqc_read_distrib_html	multiqc_read_distrib_html	n/a	File
multiqc_reads_per_chrom_html	multiqc_reads_per_chrom_html	n/a	File
multiqc_gene_body_cov_html	multiqc_gene_body_cov_html	n/a	File
multiqc_dup_html	multiqc_dup_html	n/a	File
inferexperiment	inferexperiment	n/a	File
pgt	pgt	n/a	File
multiqc_star_counts_html	multiqc_star_counts_html	n/a	File
counts_from_star	counts_from_star	n/a	File
counts_from_star_sorted	counts_from_star_sorted	n/a	File
Gene length	Gene length	n/a	File
featureCounts_sorted	featureCounts_sorted	n/a	File
featureCounts_gene_length	featureCounts_gene_length	n/a	File
multiqc_featureCounts_html	multiqc_featureCounts_html	n/a	File
featureCounts	featureCounts	n/a	File

QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows
11.0

Associated Tutorial

Features

Thanks to...

Inputs

Steps

Outputs

Version History

11.0 (earliest) Created 2nd Jun 2025 at 11:05 by GTN Bot

Creators

Submitter

QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows 11.0

Associated Tutorial

Features

Thanks to...

Inputs

Steps

Outputs

Version History

11.0 (earliest) Created 2nd Jun 2025 at 11:05 by GTN Bot

Creators

Submitter

Related items

QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows
11.0