RNA-seq III  (De Novo Transcriptome Assembly using Trinity)

RNA-seq III  (De Novo Transcriptome Assembly using Trinity) aims to provide an introduction to transcriptome assembly from Illumina RNA-seq reads using Trinity software (https://github.com/trinityrnaseq/).

The workshop is centered around hands-on exercises performed by participants with step-by-step instructions, and will facilitate better understanding of the de novo assembly processes and subsequent analysis.

Intro to Hi-C

Higher-order chromatin structure is being increasingly recognized as a critical component of gene regulation. Long-range chromatin interactions can be detected using Hi-C, a genome-wide derivative of the chromosome conformation capture (3C) assay. This three-day workshop is designed to provide an introduction to Hi-C analysis.

Intro to Phylogenetics

This workshop presents the scientific basis behind the different approaches in phylogenetics and the tools used for these analyses. Practical aspects of the use of these tools will be discussed.


A three-day workshop for hands-on analysis of genome-wide DNA methylation profiles. In this workshop, we will learn about various tools available for WGBS data analysis, including alignment, methylation calling, identification of differentially methylated regions (DMRs), and visualization. The workshop will include hands-on learning and in-depth discussion of experimental design, data interpretation, advantages and disadvantages of multiple tools.

RAD-Seq Analysis

Restriction site Associated DNA Sequencing (RAD-Seq) sequences short regions immediately flanking restriction sites. RAD-Seq enables cost-effective marker discovery and genotyping of hundreds of thousands of genetic markers in hundreds of samples in ANY species, with or without a reference genome. This three-day workshop will practice hands-on analysis of RAD-Seq data. We will use popular stacks pipeline (http://catchenlab.life.illinois.edu/stacks/) to de novo assemble RAD loci for species lacking a reference genome


MERFISH and seqFISH are new techniques for measuring 100s to 1000s of gene expression levels in-situ with high sensitivity and specificity. This workshop covers a detailed introduction to the methodology, and what goes into experimental design/execution.