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Review
. 2020 Mar-Apr;17(2):566-586.
doi: 10.1109/TCBB.2018.2873010. Epub 2018 Oct 1.

Differential Expression Analysis of RNA-seq Reads: Overview, Taxonomy, and Tools

Hussain Ahmed Chowdhury, Dhruba Kumar Bhattacharyya, Jugal Kumar Kalita
Review

Differential Expression Analysis of RNA-seq Reads: Overview, Taxonomy, and Tools

Hussain Ahmed Chowdhury et al. IEEE/ACM Trans Comput Biol Bioinform. 2020 Mar-Apr.

Abstract

Analysis of RNA-sequence (RNA-seq) data is widely used in transcriptomic studies and it has many applications. We review RNA-seq data analysis from RNA-seq reads to the results of differential expression analysis. In addition, we perform a descriptive comparison of tools used in each step of RNA-seq data analysis along with a discussion of important characteristics of these tools. A taxonomy of tools is also provided. A discussion of issues in quality control and visualization of RNA-seq data is also included along with useful tools. Finally, we provide some guidelines for the RNA-seq data analyst, along with research issues and challenges which should be addressed.

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