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Center for Infectious Disease and Vector Research



Events Calendar


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

Thomas Girke

Saturday, December 14, 2013
9 a.m.12:30 p.m.

Location:

Genomics Building , Auditorium
Parking Information

Description:

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.  Maximum number of participants: 40 [ Schedule and Teaching Material ]     

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 organizations and academic institutions outside of the US.

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

Admission:

Reservations Required

Sponsor:

Institute for Integrative Genome Biology


More Information

General Campus Information

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

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Department Information

Institute of Integrative Genomics Biology
2150 Batchelor Hall

Tel: (951) 827-7177

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