RNA sequencing data analysis software tools

RNA sequencing (RNA-seq) also known as whole transcriptome shotgun sequencing (WTSS) is the next-generation sequencing technology to study the transcriptome. It could be used as an alternative to microarrays for gene expression analysis, without the need to know the RNA sequence a priori. RNA-seq offers more accurate data and applications including detection of gene fusion, variants, alternative splicing, post-transcriptional modifications as well as for analysis of small RNAs such as tRNA or miRNA profiles. A complete picture of the RNA content can be obtained from low quantity biological samples. Several analytical steps are critical for a successful characterization and quantification of the transcriptome. A large list of bioinformatic tools is proposed here for quality control, data processing, quantification, annotation and visualization as well as for interpretation and biological network analysis for understanding RNA-seq data.

Data preprocessing

Data processing


Data analysis


Survival analysis

Splicing events

Protein sequence/Expression

Membrane protein


Variant effect analysis

Genome-wide association study/Linkage/QTL


Data visualization


Network analysis

Enrichment analysis

PCR/qPCR analysis

Integrative analysis


File manipulation


Unclassified tools