Consider:

This is a new book:

R Bioinformatics Cookbook: Use R and Bioconductor to perform RNAseq, genomics, data visualization, and bioinformatic analysis

http://sfg.stanford.edu/guide.html

Hi MS Hossain,

U can go through the article entitled “Introduction to RNA-seq data analysis” by Myrto Kostadima. Its well conceptualized, concise and contains all commands for performing data analysis.

Best of luck!

You could check out the book "RNA-seq Data Analysis - a practical approach" (https://www.crcpress.com/RNA-seq-Data-Analysis-A-Practical-Approach/Korpelainen-Tuimala-Somervuo-Huss-Wong/p/book/9781466595002)

It starts from scratch and gives you a general introduction into the topic, but also provides hands-on with code examples of the tools to use.

Transcriptome Data Analysis

Methods and Protocols

https://www.springer.com/gp/book/9781493977093

RNA-seq Data Analysis: A Practical Approach (Chapman & Hall/CRC Mathematical and Computational Biology)

The best video I have watched on RNA-Seq analysis:

https://www.youtube.com/watch?v=xh_wpWj0AzM

https://bioinformatics.upsc.se

A comprehensive book would be:

https://www.springer.com/gp/book/9781627037082