Large-Scale Data Workshop: Computational Methods for RNA Sequencing Analysis

Sunday, December 13, 2015
3:00 pm-6:25

Manuel Garber
UMASS Medical School

Broad Institute of Harvard and MIT

Alper Kucukural
UMASS Medical School

Broad Institute of Harvard and MIT
3:00 pm-4:00 pm

4:00 pm-6:25 pm

Didactic Overview. Open to all ASCB attendees.

Hands-on workshop. Limited to 50 participants who must pre-register. Click here or on the orange button below to login and register for the hands-on portion of this workshop. You must already be registered for the 2015 Cell Biology ASCB Annual Meeting to be able to register for this workshop. 

The workshop will focus on RNA-Seq application to gene expression. In the overview section we will describe the main computational components of gene expression analysis: 1) Alignment techniques and approaches and the impact of alignment on gene quantification; 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; 4)  Differential gene expression analysis using DESeq; and 5) Typical analysis such as gene ontology, clustering, and principal component analysis using R.

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

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 get familiar with R. We strongly suggest the R tutorial here to return to the list of workshops.