Reference-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
9.0 (latest) Created 16th Jul 2024 at 14:05 by Helena Rasche
Added/updated 4 files
Open
master
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17.0 (earliest) Created 25th Jun 2024 at 11:24 by Helena Rasche
Added/updated 4 files
Frozen
17.0
41c9464
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
Creators
Not specifiedSubmitter
Views: 252 Downloads: 113
Created: 25th Jun 2024 at 11:24
Last updated: 5th Jul 2024 at 14:24
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
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