How to analyze RNA-Seq data? Find differentially expressed genes in your research.

If you benefit from my tutorial and use the same strategy for data analysis, please CITE my RNA-Seq paper published in "Scientific Reports - Nature": https://www.nature.com/articles/s4159... And "PLOS ONE": https://journals.plos.org/plosone/art... ●Chu, C.P., Hokamp, J.A., Cianciolo, R.E. et al. RNA-seq of serial kidney biopsies obtained during progression of chronic kidney disease from dogs with X-linked hereditary nephropathy. Sci Rep 7, 16776 (2017). ●Brinkmeyer-Langford C, Chu C, Balog-Alvarez C, Yu X, Cai JJ, et al. (2018) Expression profiling of disease progression in canine model of Duchenne muscular dystrophy. PLOS ONE 13(3): e0194485. ------------------------------------ This is a class recording of VTPP 638 "Analysis of Genomic Signals" at Texas A&M University. No RNA-Seq background is needed, and it comes with a lot of free resources that help you learn how to do RNA-seq analysis. You will learn: (1) The basic concept of RNA-sequencing (2) How to design your experiment: library prep, sequencing depth, budgets, statistical power. (3) The analysis pipeline (4) Useful resources (all free!!!). Up-to-date RNA-Seq Analysis Training/Courses/Papers (Updated on Dec 2017) http://www.biostars.org/p/174376/ ------------------------------------ Other links are listed here: 1. Comparison of different Illumina Truseq RNA Prep kits: http://www.illumina.com/documents/pro... 2. Scotty-Power analysis for RNA Seq Experiments: http://scotty.genetics.utah.edu/ 3. Illumina Sequencing Technology:    • Illumina Sequencing Technology   4. Ensembl FTP download website (include file format description): http://useast.ensembl.org/info/data/f... 5. HISAT2: https://ccb.jhu.edu/software/hisat2/i... 6. HTSeq: http://www-huber.embl.de/users/anders... 7. DESeq2 (click on "PDF" for manual): http://bioconductor.org/packages/rele... 8. How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? http://rnajournal.cshlp.org/content/2... 9. Gene Ontology: http://pantherdb.org/ 10. IPA Webinars: https://www.qiagenbioinformatics.com/... 11. Texas A&M Supercomputing Facility-trainings: https://sc.tamu.edu/wiki/index.php/HP... 12. Command Line Tools for Genomic Data Science: https://www.coursera.org/learn/genomi... 13. Informatics for RNA-Seq Analysis 2016:    • Informatics for RNA-Seq Analysis 2016   14. http://www.rnaseq.wiki/ 15. Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud: http://journals.plos.org/ploscompbiol... 16. A survey of best practices for RNA-seq data analysis: https://genomebiology.biomedcentral.c... 17. RNA-Seq workflow: gene-level exploratory analysis and differential expression: https://www.ncbi.nlm.nih.gov/pmc/arti... 18. RNA-Seq Blog: http://www.rna-seqblog.com/ 19. BioStars: http://www.biostars.org/ 20. RNA-Seq Analysis Tutorial: https://github.com/CandiceChuDVM/RNA-...