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

Workflow Type: Galaxy

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

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

gtn star logo followed by the word workflows

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

Version History

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

Added/updated 4 files


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Created: 2nd Jun 2025 at 11:05

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