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April 2020

QCBio Research Seminar: Gabriel Hassler (Suchard Lab)

April 7 @ 12:00 pm - 12:30 pm

“Scalable inference in models of phenotypic evolution”  

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QCBio Research Seminar: Ying Tang (Hoffmann Lab)

April 3 @ 12:00 pm - 12:30 pm

“Quantifying information encoded in dynamical patterns of biochemical signaling"  

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March 2020

W9: Intro to Python

March 31 @ 1:30 pm - April 2 @ 4:30 pm
ZOOM CA United States + Google Map

This workshop will cover the basic concepts of Python programming. The course is supplemented with many hands-on exercises with emphasis given towards computational biology use cases.

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QCBio Research Seminar: Giovanni Quinones Valdez (Xiao Lab)

March 31 @ 12:00 pm - 12:30 pm

“A micro-InDel caller tailored for RNA-Seq data”    

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W1: Intro to Unix command line

March 31 @ 9:00 am - April 2 @ 12:00 pm
ZOOM CA United States + Google Map

Unix is a command-line-based platform that is a highly powerful and flexible tool for data management and analysis. First, this workshop introduces the basic concepts of UNIX operating system and shell scripting. We will explore essential hands-on skills to confidently use the command line interface on either a local (laptop) or a remote (hoffman2 cluster) computer running the Unix system. Next, this workshop covers how to navigate around the Unix file system from the command line and use a number…

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W8: Variant Discovery with GATK

March 10 @ 1:30 pm - March 12 @ 3:30 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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This workshop uses materials developed by the Broad Institute to teach Variant Discovery with GATK.  Attendees with no prior experience in variant calling are recommended to review all of the materials below before coming to the workshop. This early preparation will allow a focus on the specific issues of running GATK on the UCLA hoffman2 cluster rather than introducing the GATK variant calling pipeline. There will also be a focus on post variant discovery quality control steps as time allows.

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W5b: RNA-Seq II Analysis

March 10 @ 1:30 pm - March 12 @ 3:30 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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RNA-seq II aims to provide tools for analysis of gene expression data from read counts to biology using R. To facilitate learning, the workshop will use a real case study based approach appropriate for Illumina read data (same as RNA-seq I).

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QCB Research Lunch – Michael Thompson (Halperin Lab)

March 6 @ 12:30 pm - 1:00 pm
Boyer 159, 611 Charles E. Young Dr. E.
Los Angeles, CA 90095 United States
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"Disentangling heterogeneous and homogeneous genetic variability in multi-context studies"

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QCB Research Lunch – Xinzhou Ge (Li Lab)

March 6 @ 12:00 pm - 12:30 pm
Boyer 159, 611 Charles E. Young Dr. E.
Los Angeles, CA 90095 United States
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"EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences"

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W4: Galaxy for NGS Data Analysis

March 4 @ 10:00 am - March 5 @ 12:00 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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Galaxy (https://usegalaxy.org/) is a web-based infrastructure for bioinformatics application. First, this workshop introduces participants to using Galaxy for analysis of Next-Generation Sequencing data. Next, this workshop covers the structure of Galaxy, data format and manipulation, obtaining and sharing data, and building and sharing workflows. We will use the tools installed on the UCLA galaxy to perform a few types of NGS analysis.

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