https://sagc-bioinformatics.github.io/workshop_nfRNAseq/
Thursday 10 October 2024 10:00am - 4:00pm
A practical guide to RNAseq analysis, using nextflow-core pipelines (https://nf-co.re/) as a platform to guide participants through key analyses.
RNAseq is a staple methodology for molecular and genetic research. Key to the success of RNAseq has been the development of a suite of computational biology tools for its analysis. Recent initiatives to collect and publish curated analysis pipelines such as nf-core, are consolidating decades of software development. Made possible by the development and increasing popularity of nextflow, a workflow management system. Effectively making analysis options of many genomics technologies including RNAseq, more accessible, reproducible, and streamlined.
- A hands-on walk-through of nf-core analysis pipelines for RNAseq:
- nf-core/RNAseq ; Mapping and counting NGS data, QC metrics
- nf-core/DifferentialAbundance ; differential expression analysis
- Run nf-core pipelines; including installation and config setup
- Description of the key metrics and analyses for RNAseq analysis
- Descriptions of key genomic file formats used for RNAseq analysis
- deployment of an R-shiny app
- Gain familiarity with key tools and pipelines nf-core, and how to decipher the outputs
Anyone using or intending to analyse RNAseq data. The goal is to make it approachable to those new to RNAseq, but also broad and detailed enough to keep established users informed and interested.
By nature it is going to be a computational biology focus and will include using unix/R/HPC/Nextflow tools and commands. But since the focus will be on understanding each process of the analysis, describing the results and how to use them, this is meant to be approachable to those using RNAseq for research or diagnostics, who aren’t necessarily bioinformaticians.
Flinders City Campus (Festival Tower) Room 505
The username and password for wifi access at the Flinders City camputs
For those who have it, eduroam should be available as well
user = Flinders Conference
password = goldjade63
| Topic | |
|---|---|
| 10:00 | setup & housekeeping |
| - access to nectar VM | |
| 10:10 | Applications of RNAseq |
| - bioinformratics tools overview | |
| 10:15 | Nextflow |
| - using nexflow run | |
| 10:45 | nf-core |
| - nf-core tools | |
| - pipelines for RNAseq | |
| 11:15 | morning tea |
| 11:30 | nf-core/RNAseq |
| - setting up/ running | |
| - understanding RNAseq files | |
| - interpreting RNAseq results | |
| 12:30 | lunch provided |
| 1:30 | nf-core/DifferentialAbundance |
| - Rshiny App | |
| 2:30 | Afternoon Tea |
| 2:45 | nf-core/smRNAseq |
| - small RNA analysis | |
| 3:45 | Experimental design |
| 4:00 | wrap up |
