How to analysis the data of RNA-Seq?

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Kandasamy Ulaganathan

Please read the following paper:

Introduction to differential gene expression analysis using RNA-seq Written by Friederike Dündar, Luce Skrabanek, Paul Zumbo September 2015 updated October 8, 2018 (PDF copy attached)

Pedro de los Reyes Rodríguez

If you have the raw data from the RNA-sequencing and basic concepts of bioinformatics, you can analyze it with the 'new Tuxedo' protocol. Easy and fast.

https://www.nature.com/articles/nprot.2016.095

Good luck,

Pedro.

Fabrice Chatonnet

You have a quantity of tools, either in command line or online to analyze RNA-seq data, and probably some bio-informaticians near you to get some help... See https://usegalaxy.org for example, or some general reviews about RNA-seq analysis.

Jiaojiao Liu

thank you very much! And I want to use this website to draw a heatmap, but the raw data is FPKM, how to get the p values, especially these values of control group? looking forward to your reply!@Fabrice Chatonnet

I'm not sure that I get your question right, but if you want to draw a heatmap, you need to do it on expression values, not on p-values which are a statistical tool to determine if your genes are significantly differentially expressed (DE) or not (between two or more conditions). What you can do is select only DE genes and then perform a heatmap of DE genes expression, for that one of the easiest way is to use R software. It's dedicated to statistics and graphics and you can find a lot of help on internet. Functions like heatmap.2() in the gplots package usually does the job very well (with a few settings). Good luck!