mRNA-Seq BY-COVID Pipeline Version 1
Analyse Bulk RNA-Seq data in preparation for downstream Pathways analysis with MINERVA
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| mRNA-Seq Reads | n/a | Input list of fastqsanger format sequencing data |
|
| UCSC Genome | n/a | Export of UCSC Genome, just the genes. |
|
| factordata | n/a | A two column factor table with (Sample Identifier, Condition) This workflow assumes a 1 factor, 2 level analysis, and was specifically designed around SARS-CoV-2 analysis with two levels, e.g. ``` SampleName Group SRR16683284 COVID SRR16683283 COVID SRR16683271 healthy SRR16683270 healthy ``` |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | n/a | n/a |
| 4 | n/a | n/a |
| 5 | n/a | n/a |
| 6 | n/a | n/a |
| 7 | n/a | n/a |
| 8 | n/a | n/a |
| 9 | n/a | n/a |
| 10 | n/a | n/a |
| Gene Lengths | n/a | n/a |
| Multi QC raw reads | n/a | n/a |
| countdata | n/a | n/a |
| annodata | n/a | n/a |
| 15 | n/a | n/a |
| limma DEG analysis | n/a | n/a |
| 17 | n/a | n/a |
| 18 | n/a | n/a |
| MINERVA Formatting | n/a | n/a |
| 20 | n/a | n/a |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| html_report | n/a | n/a |
|
| count_data | n/a | n/a |
|
| limma_report | n/a | n/a |
|
| minerva_table | n/a | n/a |
|
Version History
Version 1 (earliest) Created 6th Dec 2023 at 13:38 by Helena Rasche
Added/updated 966 files
Open
master46393c2
Creators and Submitter
Views: 6270 Downloads: 0
Created: 6th Dec 2023 at 13:38
Last updated: 6th Dec 2023 at 13:47
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BY-COVID related wo...
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https://orcid.org/0000-0001-9760-8992Failure is not an option.
借屍還魂
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
canonical record: https://zenodo.org/records/10405036
Source data (GSE182152) was analysed with WFHub:688 to generate these datasets
Creators: Helena Rasche, Iacopo Cristoferi, Marek Ostaszewski, Andrew Stubbs
Submitter: Helena Rasche
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Workflows developed by or used by BY-COVID project.
