Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.

ABSTRACT: High-throughput sequencing of mRNA (RNA-seq) has become the standard method for measuring and comparing the levels of gene expression in a wide variety of species and conditions. RNA-seq experiments generate very large, complex data sets that demand fast, accurate and flexible software to reduce the raw read data to comprehensible results. HISAT (hierarchical indexing for spliced alignment of transcripts), StringTie and Ballgown are free, open-source software tools for comprehensive analysis of RNA-seq experiments. Together, they allow scientists to align reads to a genome, assemble transcripts including novel splice variants, compute the abundance of these transcripts in each sample and compare experiments to identify differentially expressed genes and transcripts. This protocol describes

SUBMITTER: Pertea M 

PROVIDER: S-EPMC5032908 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature