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Fill in bullet point 4 on "Request for Umass RStudio server account/ install local Rstudio"

Section 1:

The Unix Tutorial Part 2: (Piping &) Shell Scripting
"Getting Data for Analysis" page
Analysis of FASTQC report
Trimmomatic > IGV pre-analysis and post-analysis

Section 2:

Tophat2 + Cufflinks + Cuffmerge

Section 3:

Visualization

Bioinformatics Workshop: A tutorial on RNA-Seq Data Analysis on MGHPCC

Welcome to the bioinformatics workshop on RNA-seq data analysis. This page contains the materials and links to materials that you will need for the workshop.

General Information

This 2-day workshop aims to equip life-scientists with basic lab skills for scientific computing and to provide an introduction to RNA-seq data analysis followed by tutorials demonstrating the use of popular RNA-seq analysis packages. It will cover basic concepts and tools to leverage HPC environment (i.e. Linux and LSF command). Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

By the end of the workshop, participants will gain practical experience and skills to be able to:

Recognize input and output file formats commonly used in RNA-seq data analysis
Identify the major analysis steps in a typical RNA-seq data analysis pipeline
Demonstrate a working example of RNA-seq data analysis pipeline based on Tuxedo protocol (Trapnell et al. 2012) using command-line software on Linux cluster environment (i.e MGHPCC)

The learning objectives of the workshop are:

Understand major analysis components and standard tools used in a typical RNA-seq data analysis workflow
Construct a workflow to answer specific research questions
Evaluate and integrate new bioinformatics tools into a workflow

Who

Undergraduates, graduates, postgraduates, and PIs working on analysis of RNA-seq data.

Where TBD

Prerequisites for attendance

**You must have a UMass MGHPCC account to participate in the workshop. Follow the instructions here to request for an account from the MGHPCC Team and Research Computing/ Information Services at UMass Medical School. The request could take 1-5 business days to complete so be sure to plan ahead.
Fill in this Registration Form (Link to Google Form) after registering for your MGHPCC account.
Please bring your own laptop.
Request for Umass RStudio server account/ Installing R and RStudio on local computer.
Please complete the following simple Unix, Git, and R tutorials before attending:-

a. UNIX Tutorial for Beginners. (Tutorial 1-4)

b. Try the tutorial here to start learning R

c. Git is a version control system for tracking changes to files.

You may have used SVN, an older version control system. git is different in some important ways: git is distributed: everyone has a copy of the repository, so you can work offline and things happen fast. git is all about a branch-based workflow.

Here is an 15 min interactive tutorial to give you the basics.