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February 2021

W6: DNA Methylation Analysis with R and Unix

February 23 @ 9:00 am - February 25 @ 12:00 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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This workshop will introduce the basic principles of DNA methylation and briefly describe available methods for DNA methylation assessment, focusing on bisulfite sequencing (BSseq). We will cover the principles of BSseq preprocessing, alignment and methylation calling, differential methylation analysis, annotation and visualization. Attendees will  have the opportunity to work on real DNA methylation data provided by the instructor and run the analysis on Hoffman2 and locally. Attendees need to have a basic knowledge in UNIX commands and R programming for…

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W5a: RNA-seq I Analysis

February 23 @ 1:30 pm - February 25 @ 4:30 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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RNA-seq I aims to provide an introduction and the basics tools to process raw RNA-seq data on a cluster machine (Hoffman2). The workshop can serve also as a starting point to develop a gene expression project. This workshop is divided in three days that will cover major steps of processing RNA-seq. To facilitate learning, the workshop will be centered on hands-on tutorial that will guide students in processing the data from raw reads through read counts using a real case…

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March 2021

W5b: RNA-Seq II Analysis

March 2 @ 9:00 am - March 3 @ 11:00 am
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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W8: Variant Calling with GATK

March 2 @ 1:30 pm - March 4 @ 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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