RNA-Seq Analyses In Non-Model Organisms (Virtual Course)
RNA-Seq technology has been transformative in our ability to explore gene content and gene expression in all realms of biology, and de novo transcriptome assembly has enabled opportunities to expand transcriptome analysis to non-model organisms. This workshop provides an overview of modern applications of transcriptome sequencing and popular tools and algorithms for exploring transcript reconstruction and expression analysis in a genome-free manner, leveraging the Trinity software and analysis framework. Attendees will perform quality assessment of Illumina RNA-Seq data, assemble a transcriptome using, among others, Trinity, quantify transcript expression, leverage Bioconductor tools for differential expression analysis, and apply Trinotate to functionally annotate transcripts. In parallel to the short-read assembly, participants will perform the pre-processing of 3rd generation sequencing data (PacBio IsoSeq) and the resulting assemblies will be compared. Additional methods will then be explored for characterizing the assembled transcriptome and revealing biological findings. Due to the COVID-19 outbreak, this course will be held online.