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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

Category: Training

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.

Open to: General Public
Admission: Reservations Required:
Sponsor: Institute for Integrative Genome Biology

Contact Information:
Guille Vallejo

guille.vallejo@ucr.edu