Related Experiment Video
Updated: Mar 26, 2026
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
Published on: June 8, 2020
A survey of best practices for RNA-seq data analysis
Ana Conesa1,2, Pedro Madrigal3,4, Sonia Tarazona5,6
1Institute for Food and Agricultural Sciences, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32603, USA. aconesa@ufl.edu.
Abstract:
RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.
Related Concept Videos
03:21RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
02:24Ribosome Profiling
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...