In this section, we will use bioinformatic and computational approaches to analyze our Pol II ChIP-seq data sets.
We will discuss the details of the experimental approaches and rationale for experimental design. Students will be guided through analysis using software packages and excel, using computers set up in the lab. We will also apply a set of web-based bioinformatic tools to the data analyses. Finally, for those who are interested, we will meet in small groups to discuss the implementation of R scripts, and command line data analysis tools.
This module is, by its nature, free flowing and subject to adjustments “on the fly”. Thus, we have not included any definitive materials for you in this manual. Rather, you will be provided with all of the information you need in the computer lab.
The approaches we will cover are as follows:
A. Basics of genomic analysis of RNA-seq and ChIP-seq data
B. User interface-based genomic data analyses
C. Web-based tools for the analysis of genomic data sets.
GeneX CSHL 