Welcome
If you are considering adventuring through the realm of bioinformatics and transcriptome analyses but don't know how or where to start, don't panic! We've got your back.
Schedule Overview
Part 1: Don't panic: A survival guide to RNA-Seq. March 9, 2021, from 3:00 pm to 3:45 pm (EST)
Part 2: Don't panic again: Training for RNA-Seq battles. March 16, 2021, from 3:00 pm to 4:00 pm (EST)
How does it work?
Part 1 - Theory
March 9, 2021, from 3:00 PM to 3:45 PM (EST)
On this first day, we will provide attendees (that perhaps have no prior training in these sequencing and bioinformatic techniques) a basic guideline to RNA-Seq, from experimental design to data interpretation in the context of the p-value crises.
Part 2 - Practice
March 16, 2021, from 3:00 pm to 4:00 pm (EST)
We will follow a basic pipeline (from quality control to gene expression analysis) using free software in a Unix-based framework (such as a personal MacBook). Denis will be available 30 min before the event to assist participants in getting ready to follow the exercises in real-time. Attendees may choose to follow the exercises with Denis or simply watch as he moves through the different steps of RNA-Seq on his screen. Click on the button below to download an image with all the materials inside. Click here to learn how to import an appliance in VirtualBox.
Computational Requirements
Every participant will need a personal computer with about 50 GB of free disk space, at least 4 GB of memory or more, and at least 2 processors/threads. Most personal computers that are younger than six years old should meet the systems requirements. There are no operating system restrictions. Instructions to download and install Oracle's VM VirtualBox and the image with the course material will be available here shortly. Click here to download an image with all the materials inside. Click here to learn how to import an appliance in VirtualBox.
References
Brown, S. M. (Ed.). (2015). Next-generation DNA sequencing informatics. New York, NY: Cold Spring Harbor Laboratory Press.
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., ... & Regev, A. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29(7), 644. https://www.nature.com/articles/nbt.1883
Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., ... & Regev, A. (2013). De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols, 8(8), 1494-1512. https://www.nature.com/articles/nprot.2013.084
Koch, C. M., Chiu, S. F., Akbarpour, M., Bharat, A., Ridge, K. M., Bartom, E. T., & Winter, D. R. (2018). A beginner’s guide to analysis of RNA sequencing data. American Journal of Respiratory Cell and Molecular Biology, 59(2), 145-157. https://doi.org/10.1165/rcmb.2017-0430TR
Lamarre, S., Frasse, P., Zouine, M., Labourdette, D., Sainderichin, E., Hu, G., ... & Maza, E. (2018). Optimization of an RNA-Seq differential gene expression analysis depending on biological replicate number and library size. Frontiers in Plant Science, 9, 108. https://www.frontiersin.org/articles/10.3389/fpls.2018.00108/full
Mashanov, V., Akiona, J., Khoury, M., Ferrier, J., Reid, R., Machado, D. J., ... & Janies, D. (2020). Active Notch signaling is required for arm regeneration in a brittle star. PloS one, 15(5), e0232981. https://doi.org/10.1371/journal.pone.0232981
Schurch, N. J., Schofield, P., Gierliński, M., Cole, C., Sherstnev, A., Singh, V., ... & Barton, G. J. (2016). How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA, 22(6), 839-851. https://rnajournal.cshlp.org/content/22/6/839
Van den Berge, K., Hembach, K. M., Soneson, C., Tiberi, S., Clement, L., Love, M. I., ... & Robinson, M. D. (2019). RNA sequencing data: hitchhiker's guide to expression analysis. Annual Review of Biomedical Data Science, 2:139-173. https://doi.org/10.1146/annurev-biodatasci-072018-021255
Zhao, S., Ye, Z., & Stanton, R. (2020). Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols. RNA, 26(8), 903-909. https://rnajournal.cshlp.org/content/early/2020/04/13/rna.074922.120
Meet you instructor
Denis Jacob Machado, Ph.D.
Department of Bioinformatics and Genomics
University of North Carolina at Charlotte
Watch the recording of the first part of the workshop
March 9, 2021
On this first day, we provided attendees (that perhaps have no prior training in these sequencing and bioinformatic techniques) a basic guideline to RNA-Seq, from experimental design to data interpretation in the context of the p-value crises.
Watch the recording of the second part of the workshop
March 16, 2021
In the second part of this workshop, we took a look at real data using materials from a VirtualBox image created just for you to practice some basic bioinformatic skills.