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": www.nature.com...
And "PLOS ONE": journals.plos....
●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.
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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)
www.biostars.or...
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Other links are listed here:
1. Comparison of different Illumina Truseq RNA Prep kits:
www.illumina.co...
2. Scotty-Power analysis for RNA Seq Experiments:
scotty.genetics...
3. Illumina Sequencing Technology:
• Illumina Sequencing Te...
4. Ensembl FTP download website (include file format description):
useast.ensembl....
5. HISAT2: ccb.jhu.edu/so...
6. HTSeq:
www-huber.embl....
7. DESeq2 (click on "PDF" for manual):
bioconductor.or...
8. How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?
rnajournal.cshl...
9. Gene Ontology: pantherdb.org/
10. IPA Webinars:
www.qiagenbioi...
11. Texas A&M Supercomputing Facility-trainings:
sc.tamu.edu/wi...
12. Command Line Tools for Genomic Data Science:
www.coursera.o...
13. Informatics for RNA-Seq Analysis 2016:
• Informatics for RNA-Se...
14. www.rnaseq.wiki/
15. Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud:
journals.plos.o...
16. A survey of best practices for RNA-seq data analysis:
genomebiology....
17. RNA-Seq workflow: gene-level exploratory analysis and differential expression:
www.ncbi.nlm.n...
18. RNA-Seq Blog: www.rna-seqblog...
19. BioStars: www.biostars.org/
20. RNA-Seq Analysis Tutorial:
github.com/Can...