{Reference Type}: Journal Article
{Title}: Plant Transcriptome Analysis with HISAT-StringTie-Ballgown and TopHat-Cufflinks Pipelines.
{Author}: Rao X;
{Journal}: Methods Mol Biol
{Volume}: 2812
{Issue}: 0
{Year}: 2024
暂无{DOI}: 10.1007/978-1-0716-3886-6_11
{Abstract}: 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.