Center for Infectious Disease and Vector Research

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Bioinformatics Workshop: Analysis of ChIP-Seq Data with R/Bioconductor

Thomas Girke

Sunday, December 9, 2012
9 a.m.12:30 p.m.


Genomics Building , Genomics Auditorium, RM 1102A
Parking Information


Description: This workshop will cover the most common ChIP-Seq data analysis routines. It will include the following topics: (1) short read alignment against reference genomes; (2) efficient handling of read coverage data; (3) peak calling with various algorithms implemented in R; (4) integration of data from external peak callers; (5) annotating peaks with genomic context information; (5) statistical analysis of differential binding; (6) peak viewing using R graphics and the IGV genome browser; (7) identification of enriched DNA motifs in peak sequences. Basic knowledge of the R software including sequence handling routines, as introduced in the "Introduction to R" and Basic NGS tutorials, will be expected in this workshop.  Manual for this workshop
Maximum number of participants: 40

How to sign up: send chosen workshop date, your name, email address, title of your position, lab affiliation (PI) and department information to thomas.girke@ucr.edu.

Registration fee*: no charge for participants from registered labs, $23 for UCR members, $75 for participants from external academic institutions, and $102 for participants from commercial institutions.

Laptop requirements: Participants will work during the course on a Linux cluster. Personal laptops are required to log remotely into the cluster. For this, all laptops need to have a functional wireless connection. In addition, they will need a terminal application and a SCP software for file exchange. Windows users should install for this purpose PuTTY and WinSCP. On Mac OS X systems, one can use the native terminal application and Fugu for file exchange. Linux systems usually have similar applications pre-configured

Additional Information:

Open to:

General Public



Institute for Integrative Genome Biology


Thomas Girke

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University of California, Riverside
900 University Ave.
Riverside, CA 92521
Tel: (951) 827-1012

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Institute of Integrative Genomics Biology
2150 Batchelor Hall

Tel: (951) 827-7177