High-throughput sequencing technology involves a number of concepts and techniques that shape a project before application-specific processes are utilized. First, this workshop introduces the more “universal” aspects of high-throughput sequence analysis—from experimental design to sequencing and alignment methods. Next, this workshop covers common file formats for sequence data and limitations of sequencing technologies. We will explore a hands-on exercise using the Hoffman2 cluster and will use programs designed to analyze read data, clean artifact and low-quality sequences, and align short…

This workshop will cover the basic concepts of Python programming. The course is supplemented with many hands-on exercises with emphasis given towards computational biology use cases.

Unix is a command-line-based platform that is a highly powerful and flexible tool for data management and analysis. First, this workshop introduces the basic concepts of UNIX operating system and shell scripting. We will explore essential hands-on skills to confidently use the command line interface on either a local (laptop) or a remote (hoffman2 cluster) computer running the Unix system. Next, this workshop covers how to navigate around the Unix file system from the command line and use a number…

This workshop aims to provide skills needed to address experimental reproducibility, sequencing depth, data reporting and quality assessment of ChIP-seq data. Students will have opportunities to practice hands-on with state-of-the-art analytical tools.

This workshop will cover the basis of Next-Gen Sequencing Library Preparation for Illumina Sequencers. Different Library Preparation Techniques (DNA-seq, ChIP-seq, RNA-seq, Methyl-seq) are explained the first and second day in class. The third day, Quality Control steps of the starting input material and final libraries are performed in the Lab (TapeStation). Purification from Primer Dimers (using AMPure beads) and Library Submission is also performed on the same day. The third day is optional, sign-up is required.

MATLAB is a powerful, high-level programing language for numerical computation, visualization, and application development. This workshop will start by introducing the MATLAB environment and then cover working with arrays and matrices, loops and conditional statements, writing your own functions, working with files and visualizing your data. The final day will briefly introduce utilizing MATLAB to solve differential equations and the basics of computational systems biology modeling using MATLAB. The course is supplemented with many hands-on exercises. The workshop is suitable…