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 QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Uses subworkflows
Thanks to...
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
Workflow Author(s): Bérénice Batut, Mallory Freeberg, Mo Heydarian, Anika Erxleben, Pavankumar Videm, Clemens Blank, Maria Doyle, Nicola Soranzo, Peter van Heusden, Lucille Delisle
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 | 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 |
|
| 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
10.0 (latest) Created 28th Oct 2024 at 13:08 by Helena Rasche
Added/updated 4 files
Open
master9278405
17.0 (earliest) Created 25th Jun 2024 at 11:24 by Helena Rasche
Added/updated 4 files
Frozen
17.041c9464
Creators and Submitter
Views: 920 Downloads: 339
Created: 25th Jun 2024 at 11:24
Last updated: 28th Oct 2024 at 13:08
Tags AttributionsNone
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