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

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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

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1323?version=4

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 FastQC 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_fastqc_html multiqc_fastqc_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

10.0 (latest) Created 28th Oct 2024 at 13:08 by Helena Rasche

Added/updated 4 files


Open master 9278405

9.0 Created 16th Jul 2024 at 14:05 by Helena Rasche

Added/updated 4 files


Frozen 9.0 51e55d3

19.0 Created 5th Jul 2024 at 14:24 by Helena Rasche

Added/updated 4 files


Frozen 19.0 be272f4

17.0 (earliest) Created 25th Jun 2024 at 11:24 by Helena Rasche

Added/updated 4 files


Frozen 17.0 41c9464
help Creators and Submitter
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License
MIT License
Activity

Views: 917   Downloads: 338

Created: 25th Jun 2024 at 11:24

Last updated: 28th Oct 2024 at 13:08

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Total size: 265 KB
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