PRHB

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:

  1. The quality check of raw data
  2. Data preprocessing to filter low quality bases and to trim adapter sequences
  3. Alignments of high quality reads against the reference genome
  4. Transcript abundance estimation
  5. 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


Link for the practice material answers

Linux practice materials answers: Link


Dataset to be used during the workshop

Dataset


Workshop slides (Links for each day will be active one day before)

Day 1 workshop slides: Session 1 Session 2

Day 2 workshop slide: Day 2

Day 3 workshop slide: Day 3


Workshop videos

Session 1 - FIU | Day 1

Session 1 - FIU | Day 2

Session 1 - FIU | Day 3

Session 2 - UPR | Day 1

Session 2 - UPR | Day 2

Session 2 - UPR | Day 3

Session 3 - UPR | Day 1

Session 3 - UPR | Day 2

Session 3 - UPR | Day 3



Videos of RNAseq Discussion Group Morning and Afternoon Sessions; January 30, 2021



Contacts

Rosanna Giordano (rgiordano500@gmail.com) - For all other questions

Ravi Kiran Donthu (donthuanalyst@gmail.com) - For all other questions

Maria Eugenia Presa Reyes (mpres029@cs.fiu.edu) - For specific questions regarding accessing the HPC cluster

Tianyi Wang (wtian002@cs.fiu.edu) - For specific questions regarding uploading or downloading files from the workshop website