Transcriptomic Data Analysis Using the Galaxy Platform: Coffee (Coffea arabica L.) Flowers as Example

CoffeeCoffee, an important agricultural product for tropical producing countries, is facing challenges due to climate change, including periods of drought, irregular rain distribution, and high temperatures. These changes result in plant water stress, leading to significant losses in coffeeCoffee productivity and qualityQuality. Understanding the processes that affect coffeeCoffee flowering is crucial for improving productivity and qualityQuality. In this chapter, we describe a protocol for transcriptomeTranscriptomes analysis using available Internet software, mainly in the GalaxyGalaxy Platform, using RNA-SeqRNA-seq data from flowers collected from different parts of the coffeeCoffee tree. The methods presented in this chapter provide a comprehensive protocol for transcriptomeTranscriptomes analysis of differentially expressed genes from flowers of coffeeCoffee plant. This knowledge can be utilized in coffeeCoffee genetic improvement programs, particularly in the selection of cultivars that are tolerant to water deficit.