Workshop

RNASeq Analysis Workshop

November 5-7, 2020	Florida International University, Miami, Florida
November 12-14, 2020	University of Puerto Rico
November 19-21, 2020	University of Puerto Rico

Sponsors of the Workshop

Puerto Rico Science Technology and Research Trust
Department of Biology, University of Puerto Rico
Institute of Environment, NSF CREST Center for Aquatic Chemistry and Environment, Florida International University
National Science Foundation

General Information

The workshop will train participants on how to analyze RNASeq data. The training will include:

The quality check of raw data
Data preprocessing to filter low quality bases and to trim adapter sequences
Alignments of high quality reads against the reference genome
Transcript abundance estimation
Differential gene expression analysis

With the exception of the differential gene expression analysis all analyses will be done on a High Performance Computing (HPC) cluster. The differential gene expression analysis will be performed using R packages installed in individual laptops.

Workshop locations

Workshop will be held virtually for participants in Puerto Rico and Florida

Workshop schedule

The detailed schedule for the workshop can be found here: Link

Requirements

All participants of the workshop are required to possess/acquire good command of Linux and R prior to attending.

It is important that prior to attending the workshop participants study the review material that has been provided.

Each participant is required to install the following list of R packages on their laptops prior to the workshop: Link

Organizing Team

Tugrul Giray, University of Puerto Rico, San Juan, Puerto Rico, USA
Rosanna Giordano, Puerto Rico Science Technology and Research Trust, San Juan, Puerto Rico, USA
Shu-Ching Chen, Florida International University, Florida, USA
Ravi Kiran Donthu, Puerto Rico Science Technology and Research Trust, San Juan, Puerto Rico, USA
Maria Eugenia Presa Reyes, Florida International University, Florida, USA
Tianyi Wang, Florida International University, Florida, USA

Links for the review material

Linux tutorial page: Link

Linux tutorial page content in PDF format: Link

R tutorial page: Link

Very nice tutorial video on R: Link

Advanced topics on R (t-tests, anova, etc) - optional: Link

Links for the practice material

Linux practice materials: Link

Server login instructions: Link

Valuable must read papers that introduce RNAseq methods

Conesa et al. 2016 A survey of best practices for RNA-seq data analysis Link

Koch et al. 2018 A beginner’s guide to analysis of RNA sequencing data Link