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Tutorial Details: CLC Genomics Workbench Introductory Training (Lecture)

Date: Wednesday, February 19, 2014, 09:00 am - 01:00 pm
Location: 402 Walter
Instructor(s):

Instructor: Rob Mervis, CLC Bio

An Introduction to Analysis of Next Generation Sequencing Data using the CLC Genomics Workbench and Genomics Server. MSI has purchased licenses to a new commercial comprehensive bioinformatics framework, to co-exist along with the open-source Galaxy. CLC Genomics Workbench offers well-integrated easy-to-use analysis pipelines for many Next-Generation Sequencing (NGS) applications. This one-day course will be a demonstration of the types of applications and work-flows that can be performed on deep sequencing data generated by the latest instruments from Illumina, Life Technologies (SOLiD and Ion Torrent), Roche/454 and others.

Applications include the following (Please enter in the comment field up to 3 items from the itemized list below of most importance to you):

· Data import – Raw sequence reads (FASTQ, .sff etc.) and aligned reads (SAM/BAM)

· Curating reference sequences with annotations of interest

· Working with Annotation Tracks

· Read mapping to reference sequence(s) and Local Re-alignment

· Variant detection, filtering and annotation

· De novo assembly

· Transcriptome assembly

· Digital gene expression analysis by RNA Sequencing

· ChIP Seq Analysis

· Small RNA analysis

· BLAST - Find and compare genes, protein products and place contigs

· Workflows- Visually Creating and Editing Analysis Pipelines

An overview of the CLC Genomics Server including basic user-side configuration and best practice use can also be discussed, time permitting.

9 AM – noon: lecture style overview in Walter Library 402 on the above topics, highlighting the topics most requested in the comment field at registration

Noon – 1 PM: lunch, pizza will be served

1 PM – 4 PM:SEPARATE REGISTRATION Hands-on exercises in Walter Library 575. For this part, please register for tutorial titled:CLC Genomics Workbench Hands On Tutorial

Level: Introductory
Prerequisites: familiarity with biological concepts