Don't Panic: A Survival Guide to RNA-Seq
Creators: name: Machado, Denis Jacob
Publisher: name: Zenodo
Year: 2021
Subjects: subject: RNA-seq
subject: Transcriptomics
subject: Differentially expressed genes
subject: Bioinformatics
subject: FOS: Computer and information sciences
subject: FOS: Computer and information sciences

description: "Don’t Panic: A Survival Guide to RNA-Seq" is the first of a two parts workshop I was invited to give to Penn State University's students. I designed this presentation for people that are considering adventuring through the realm of bioinformatics and transcriptome analyses but don't know how or where to start. On the first day (March 9, 2021), 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 <em>p</em>-value crises. On the second day (March 16, 2021), 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). I 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 me or simply watch as he moves through the different steps of RNA-Seq on his screen. Please visit https://denisjacobmachado.wixsite.com/psu21 for more information. 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., ... &amp; Regev, A. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. <em>Nature Biotechnology</em>, 29(7), 644. https://www.nature.com/articles/nbt.1883 Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., ... &amp; Regev, A. (2013). De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. <em>Nature Protocols</em>, 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., &amp; Winter, D. R. (2018). A beginner’s guide to analysis of RNA sequencing data. <em>American Journal of Respiratory Cell and Molecular Biology</em>, 59(2), 145-157. https://doi.org/10.1165/rcmb.2017-0430TR Lamarre, S., Frasse, P., Zouine, M., Labourdette, D., Sainderichin, E., Hu, G., ... &amp; Maza, E. (2018). Optimization of an RNA-Seq differential gene expression analysis depending on biological replicate number and library size. <em>Frontiers in Plant Science</em>, 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., ... &amp; Janies, D. (2020). Active Notch signaling is required for arm regeneration in a brittle star. <em>PloS one</em>, 15(5), e0232981. https://doi.org/10.1371/journal.pone.0232981 Schurch, N. J., Schofield, P., Gierliński, M., Cole, C., Sherstnev, A., Singh, V., ... &amp; Barton, G. J. (2016). How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? <em>RNA</em>, 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., ... &amp; Robinson, M. D. (2019). RNA sequencing data: hitchhiker's guide to expression analysis. <em>Annual Review of Biomedical Data Science</em>, 2:139-173. https://doi.org/10.1146/annurev-biodatasci-072018-021255 Zhao, S., Ye, Z., &amp; Stanton, R. (2020). Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols. <em>RNA</em>, 26(8), 903-909. https://rnajournal.cshlp.org/content/early/2020/04/13/rna.074922.120
description: I would like to thank Maria Isabel da Silva for inviting me to give this two-parts workshop at PSU.