Center for Infectious Disease and Vector Research

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Bioinformatics Workshop:Basics on Analyzing Next Generation Sequencing Data with R/Bioconductor

Thomas Girke

Saturday, December 8, 2012
9 a.m.12:30 p.m.


Genomics Building , Genomics Auditorium, RM 1102A
Parking Information


Description: R and Bioconductor provide extensive utilities for analyzing sequence data from traditional and next generation sequencing technologies (e.g. Sanger or Illumina). This workshop module will cover the following topics: (1) basics on handling sequence, base call quality and annotation ranges in R; (2) demultiplexing of pooled samples; (3) generation of detailed quality reports of FASTQ files; (4) quality/adaptor trimming and filtering of reads; (5) parsing sequences by annotation ranges; (6) handling alignment and coverage objects such as SAM/BAM files in R; (7) interacting with external programs from R, such as short read aligners and peak callers; (8) read count and density analysis; and (9) genome visualization routines. Basic knowledge of the R software, as introduced in the "Introduction to R" tutorial, 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