This repository contains the U-BDS materials for the bulk RNA-seq workshop.
Workshop participants are strongly encouraged to have familiarity with Unix and R (introductory level).
The Software Carpentry provides excellent introductory level material, which can be found in the following links:
- R https://swcarpentry.github.io/r-novice-gapminder/
- Shell: https://swcarpentry.github.io/shell-novice/
If you have already attended one of the previous U-BDS workshops for R and Unix programming, then you should meet the pre-requirements. If you have not, we heavily encourage participants to go through the materials from the links above prior to attendance.
This workshop will cover the foundational topics and methods to bulk RNA-seq analysis, including:
- Introduction to raw data management and data exploration
- Secondary analysis with
nf-core/rnaseq - Tertiary analysis topics: quality and control, data normalization and differential
gene expression analysis with
DESeq2, gene annotation, gene enrichment analysis (gene-ontology and gene set enrichment analysis) - Fundamentals of data visualization for transcriptomics
While the tertiary analysis portion of the workshop is taught using personal computer (due to time limitations), a container with all R depedencies is available at: https://hub.docker.com/r/uabbds/rnaseq_workshop
Note to maintainers/authors: website rendering should always be performed with the latest version of the container. This minimizes differences in the website due to versions among tools.
- Austyn Trull
- Bharat Mishra, PhD
- Lara Ianov, PhD
A.T., B.M. and L.I. designed workshop content and initial outline. A.T. contributed to installation instructions, data management, and secondary analysis materials. B.M. contributed to Docker container creation and tertiary analysis materials (including DEG analysis, GO, WGCA, visualization etc.). L.I. supervised all work, reviewed all content and managed website design and deployment.
Nilesh Kumar, PhD and Luke Potter, PhD also provided additional edits and revisions to source material.
In addition to U-BDS's best practices and code written by U-BDS, sections of the teaching material for this workshop (parts of tertiary analysis), contains materials which have been adapted or modified from the following sources (we thank the curators and maintainers of all of these resources for their wonderful contributions, compiling the best practices, and easy to follow training guides for beginners):
- Beta phase of carpentries meterial: https://carpentries-incubator.github.io/bioc-rnaseq/index.html
- Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. doi:10.1186/s13059-014-0550-8 ; vignette: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
- Additional references and materials:
We would also like to thank the following groups for support:
- UAB's Research Computing (HPC resources and workshop logistics with resources)
- nf-core community (rnaseq pipeline)
We would also like to thank the authors of the dataset which we implement in our workshop:
- Koch CM, Chiu SF, Akbarpour M, Bharat A, Ridge KM, Bartom ET, Winter DR. A Beginner's Guide to Analysis of RNA Sequencing Data. Am J Respir Cell Mol Biol. 2018 Aug;59(2):145-157. doi: 10.1165/rcmb.2017-0430TR. PMID: 29624415; PMCID: PMC6096346.
Lastly, we would also like to thank Kristen Coutinho for the dataset suggestion, and preliminary discussions for this workshop.