RNA sequencing data analysis software tools

RNA sequencing data analysis software tools RNA sequencing (RNA-seq) is the next-generation sequencing technology to study the transcriptome. It is 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. Bioinformatic tools are 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



Survival analysis

Splicing events

Protein sequence/Expression

Membrane protein

Data analysis


Variant effect analysis

Genome-wide association study/Linkage/QTL


Data visualization


Network analysis

Enrichment analysis

PCR/qPCR analysis

Integrative analysis


File manipulation


Unclassified tools