The University of Massachusetts Amherst

Online Sequence Analysis Bootcamp for Spring 2021: Training Session

Sequence Analysis Bootcamp is for anyone interested in learning the basics of Bioinformatics with afocus on deep sequencing data analysis. 

Sequence Analysis Bootcamp for Spring 2021 will be online. There will be a preliminary meeting Thursday April 1st at 9:00am to go over what you will need in order to participate. The training sessions will begin the following Thursday, April 8th @ 9:00am via ZOOM and SLACK for approximately ½ hour and then there will be a tutorial to follow and the instructors will be available for questions and help.

The registration form can be found at:

The bootcamp will mainly focus on RNA-Seq and scRNA-Seq application to gene expression. The first two weeks, participants will get familiar with Linux and cluster environments and how to transfer data using an FTP client. The last six weeks, we will have an overview and many hands-on training sessions. In the overview sessions we will describe the main computational components of gene expression analysis:

1) Alignment techniques and approaches and the impact of alignment on gene       


2) Estimation of gene and isoform expression; and 

3) Methods to compare samples with a focus on normalization and differential gene expression analysis.

In the hands-on portion of the workshop we will rely on a previously published dataset to illustrate a full RNA-Seq analysis and the concepts discussed during the overview. We will guide participants through:

1) Quality assessment of the data;

2) Alignment;

3) Transcript quantification using the RSEM software from command line and DolphinNext interface;

4)  Differential gene expression analysis using DESeq; and

5) Typical analysis such as gene ontology, clustering, and principal component analysis using R and DEBrowser.

6) single cell RNA-Seq data processing and analysis


We expect all participants to have a laptop with internet connection capability. Many activities will require a browser; only Firefox and Chrome have been tested.

Please  request an HPCC ( account and join dolphin group (

Some activities require issuing commands on a terminal. Participants running the Windows operating system must install putty which can be downloaded from

We encourage all participants to familiarize themselves with R in advance. 

To attend the bootcamp, your lab needs to be a member of Biocore. Biocore has a $50 monthly membership fee per lab. If your lab is already a member you can join. If it is not please talk to your PI before registration. 

ZOOM link:

You will get a separate email to join the UMMS Biocore Sequence Analysis Bootcamp Slack Channel once you register.


Thursday, April 8, 2021 - 9:00am