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Workshops

Workshops on Sequencing Experiments

Slideshow PDFs: SolexaIntro1 SolexaIntro2

Description: This workshop is to introduce first-time users to our Solexa sequencing facility. The workshop will be targeted to novices and will include:

  • basic information about Solexa sequencing technology
  • sample submission process and results
  • additional data analysis services

Date: Check back for future dates

 

Special Seminar Workshop on Illumina Sequencing

When: Monday, October 19, 2009                                          
Time:  9am - 1pm                                                                                                            
Location: Genomics Auditorium, 1102A   

DESCRIPTION: 
At IIGB, the Genomics and Bioinformatics Cores are excited to be providing services and expertise in Illumina sequencing and data analysis. This massively parallel DNA sequencing technology is advancing rapidly with the continual development of new applications and ever-increasing efficiencies
in instrumentation and software.  With this in mind, the IIGB and Illumina are sponsoring a special seminar workshop with presentations from the following speakers:

 

Data Analysis Workshops

A complete list of all bioinformatics workshops offered by the facility are posted on the on the Bioinformatics Workshop page. Only workshops directly related to the analysis of HT sequencing data are listed on this page.

 

Analysis of High-Throughput Sequencing Data with R and Bioconductor
Date: Thu, July 23, 2009 (2:30-7:00pm)
Location: 1104 Batchelor Hall, UC Riverside
Instructors: Tyler Backman, Rebecca Sun & Thomas Girke
Description: R and Bioconductor provide extensive utilities for analyzing high-throughput sequencing data from next generation technologies, such as Illumina (Solexa). This workshop will cover the following topics: (1) basic sequence and string handling in R; (2) quality assessment utilities; (3) quality filtering; (4) adaptor trimming; (5) sequence alignments; (6) interacting with external alignments programs from R, e.g. SOAP, Maq, Bowtie; (7) read density and SNP analysis; and (8) visualization of genome-scale mapping data. Basic knowledge of the R software, as introduced in the tutorial Introduction into R, will be expected in this workshop. Due to the computational demands of analyzing next generation sequencing data with reasonable speed, users will work during this workshop on a Linux cluster.
Manual for this workshop
Maximum number of participants: 20
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 members from labs with an active subscription to the bioinformatics services and $75 for non-registered participants.

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.


Past Workshops


Analysis of High-Throughput Sequencing Data with R and Bioconductor
Date: Thu, March 26, 2009 (2:30-7:00pm)
Location: 1104 Batchelor Hall, UC Riverside
Instructors: Tyler Backman & Thomas Girke
Description: R and Bioconductor provide extensive utilities for analyzing high-throughput sequencing data from next generation technologies, such as Illumina (Solexa). This workshop will cover the following topics: (1) basic sequence and string handling in R; (2) quality assessment utilities; (3) quality filtering; (4) adaptor trimming; (5) sequence alignments; (6) interacting with external alignments programs from R, e.g. SOAP, Maq, Bowtie; (7) read density and SNP analysis; and (8) visualization of genome-scale mapping data. Basic knowledge of the R software, as introduced in the tutorial Introduction into R, will be expected in this workshop. Due to the computational demands of analyzing next generation sequencing data with reasonable speed, users will work during this workshop on a Linux cluster.
Manual for this workshop
Maximum number of participants: 20
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 members from labs with an active subscription to the bioinformatics services and $75 for non-registered participants.

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.

 

 

 

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