Plant Transcriptome Analysis with HISAT-StringTie-Ballgown and TopHat-Cufflinks Pipelines.

The development of next-generation sequencing technology has led to a burst of data in a single assay. Management of a large dataset requires high demands on bioinformatic skills and computing resources. Here we present two popular pipelines for RNA-seq data analysis, using open-source software tools HISAT-StringTie-Ballgown and TopHat-Cufflinks. To meet the need of plant scientist, we describe in detail how to perform such comprehensive analysis beginning with raw RNA-seq reads and available reference genome. It allows biologists to align short reads to a reference genome, measure the transcript abundance, and analyze gene differential expression under two or more conditions. We also discuss other RNA-seq tools that are comparable or alternative to this protocol.

Rao X 《-》

RNA-Seq Data Analysis for Differential Gene Expression Using HISAT2-StringTie-Ballgown Pipeline.

Comparison of transcriptome for candidate gene discovery has become an important tool for biologists. While such studies lack the degree of resolution one gets from well-designed forward or reverse genetic studies, nevertheless, this has been a method of choice for giving coarse insight into the underlying biological processes or mechanisms. This was further accelerated with the availability of sequencing technologies. While many pipelines are available for RNA-seq data analysis, the protocol discussed here will guide the first-time users for conducting routine RNA-seq analysis using whole genome sequence as reference.

Thakur V 《-》

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

Pertea M ，Kim D ，Pertea GM ，Leek JT ，Salzberg SL ... -  《-》

Analysis of RNA-Seq Data Using TopHat and Cufflinks.

Ghosh S ，Chan CK 《-》

Analysis of RNA-Seq data with TopHat and Cufflinks for genome-wide expression analysis of jasmonate-treated plants and plant cultures.

Pollier J ，Rombauts S ，Goossens A 《-》