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/s41598-017-16603-y
And "PLOS ONE": https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0194485

●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)
http://www.biostars.org/p/174376/

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Other links are listed here:

1. Comparison of different Illumina Truseq RNA Prep kits:
http://www.illumina.com/documents/products/datasheets/datasheet_truseq_stranded_rna.pdf

2. Scotty-Power analysis for RNA Seq Experiments:
http://scotty.genetics.utah.edu/

3. Illumina Sequencing Technology:
https://www.youtube.com/watch?v=womKfikWlxM

4. Ensembl FTP download website (include file format description):
http://useast.ensembl.org/info/data/ftp/index.html

5. HISAT2: https://ccb.jhu.edu/software/hisat2/index.shtml

6. HTSeq:
http://www-huber.embl.de/users/anders/HTSeq/doc/count.html

7. DESeq2 (click on "PDF" for manual):
http://bioconductor.org/packages/release/bioc/html/DESeq2.html

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/22/6/839.long

9. Gene Ontology: http://pantherdb.org/

10. IPA Webinars:
https://www.qiagenbioinformatics.com/support/webinars/

11. Texas A&M Supercomputing Facility-trainings:
https://sc.tamu.edu/wiki/index.php/HPRC:Training

12. Command Line Tools for Genomic Data Science:
https://www.coursera.org/learn/genomic-tools

13. Informatics for RNA-Seq Analysis 2016:
https://www.youtube.com/playlist?list=PL3izGL6oi0S849u7OZbX85WTyBxVdcpqx

14. http://www.rnaseq.wiki/

15. Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud:
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004393

16. A survey of best practices for RNA-seq data analysis:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8

17. RNA-Seq workflow: gene-level exploratory analysis and differential expression:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670015/

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-Seq/wiki/RNA-Seq-analysis-tutorial

Видео How to analyze RNA-Seq data? Find differentially expressed genes in your research. канала Candice Chu, DVM, PhD