QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows
Visit source
Download RO-Crate
Run on GalaxyReference-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
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: 2508 Downloads: 1145 Runs: 0
Created: 25th Jun 2024 at 11:24
Last updated: 17th Feb 2025 at 13:09
Tags AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service, Hu's Test, test 705c32e038d0, Workshop Mar 2025 Test Out, Genomics for Australian Plants, Testing RO-crate generation and submission, BSC Dev, LS Test Team, CSB, MyTestTeam
Web page: Not specified
Space: General
Public web page: https://galaxy.training
