QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows
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Download RO-CrateReference-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
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz | Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz | gtf with genes |
|
| Paired list collection with PE fastqs | Paired list collection with PE fastqs | input fastqs |
|
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 |
|
| multiqc_cutadapt_html | multiqc_cutadapt_html | n/a |
|
| multiqc_star_html | multiqc_star_html | n/a |
|
| STAR_BAM | STAR_BAM | n/a |
|
| multiqc_read_distrib_html | multiqc_read_distrib_html | n/a |
|
| multiqc_reads_per_chrom_html | multiqc_reads_per_chrom_html | n/a |
|
| multiqc_gene_body_cov_html | multiqc_gene_body_cov_html | n/a |
|
| multiqc_dup_html | multiqc_dup_html | n/a |
|
| inferexperiment | inferexperiment | n/a |
|
| pgt | pgt | n/a |
|
| multiqc_star_counts_html | multiqc_star_counts_html | n/a |
|
| counts_from_star | counts_from_star | n/a |
|
| counts_from_star_sorted | counts_from_star_sorted | n/a |
|
| Gene length | Gene length | n/a |
|
| featureCounts_sorted | featureCounts_sorted | n/a |
|
| featureCounts_gene_length | featureCounts_gene_length | n/a |
|
| multiqc_featureCounts_html | multiqc_featureCounts_html | n/a |
|
| featureCounts | featureCounts | n/a |
|
Version History
11.0 (latest) Created 17th Feb 2025 at 13:09 by Helena Rasche
Added/updated 4 files
Open
master6123676
17.0 (earliest) Created 25th Jun 2024 at 11:24 by Helena Rasche
Added/updated 4 files
Frozen
17.041c9464
Creators and Submitter
Views: 1208 Downloads: 438
Created: 25th Jun 2024 at 11:24
Last updated: 17th Feb 2025 at 13:09
Tags AttributionsNone
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