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October 2019

W12: Intro to MATLAB

October 22 @ 9:30 am - October 24 @ 12:30 pm
525 Boyer Hall,, 611 Charles E Young Dr E,
Los Angeles, CA 90095
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MATLAB is a powerful, high-level programing language for numerical computation, visualization, and application development. This workshop will start by introducing the MATLAB environment and then cover working with arrays and matrices, loops and conditional statements, writing your own functions, working with files and visualizing your data. The final day will briefly introduce utilizing MATLAB to solve differential equations and the basics of computational systems biology modeling using MATLAB. The course is supplemented with many hands-on exercises. The workshop is suitable…

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W5a: RNA-seq I Analysis

October 22 @ 1:30 pm - October 24 @ 3:30 pm
525 Boyer Hall,, 611 Charles E Young Dr E,
Los Angeles, CA 90095
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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.

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W16: Library Prep for NGS

October 29 @ 9:30 am - October 31 @ 12:30 pm
525 Boyer Hall,, 611 Charles E Young Dr E,
Los Angeles, CA 90095
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This workshop will cover the basis of Next-Gen Sequencing Library Preparation for Illumina Sequencers. Different Library Preparation Techniques (DNA-seq, ChIP-seq, RNA-seq, Methyl-seq) are explained the first and second day in class. The third day, Quality Control steps of the starting input material and final libraries are performed in the Lab (TapeStation). Purification from Primer Dimers (using AMPure beads) and Library Submission is also performed on the same day.

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W5b: RNA-Seq II Analysis

October 29 @ 1:30 pm - October 30 @ 3:30 pm

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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November 2019

W21: Digital Imaging Processing in Python

November 5 @ 9:00 am - November 7 @ 12:00 pm
525 Boyer Hall,, 611 Charles E Young Dr E,
Los Angeles, CA 90095
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Imaging datasets are becoming easier to acquire and more difficult to analyze. This workshop will provide an introduction to some of the computational tools available for manipulating images and extracting quantitative information from them. The main focus of this workshop will be on cellular imaging however much of the techniques are broadly applicable to other data types. We will cover image conversion and handling in python, different methods for normalizing, aligning and segmenting images and finally work on applying these…

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W20: Single-Cell RNA-Seq Analysis

November 5 @ 1:30 pm - November 7 @ 4:30 pm
525 Boyer Hall,, 611 Charles E Young Dr E,
Los Angeles, CA 90095
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This workshop aims to provide an entry-level introduction to the basic concepts and data analysis tools for single-cell RNA-seq techniques. It will help the attenders obtain a better idea of the important applications of scRNA-seq, the important considerations in designing a scRNA-seq experiment, the major differences between popular technical platforms, and the main steps in preliminary data analysis. It can serve as a starting point to conceive a scRNA-seq study or to analyze a scRNA-seq dataset.

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W7: ChiP-seq Analysis

November 12 @ 1:30 pm - November 14 @ 4:30 pm
525 Boyer Hall,, 611 Charles E Young Dr E,
Los Angeles, CA 90095
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This workshop aims to provide skills needed to address experimental reproducibility, sequencing depth, data reporting and quality assessment of ChIP-seq data. Students will have opportunities to practice hands-on with state-of-the-art analytical tools.

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W23: DNA Methylation Analysis

November 19 @ 9:30 am - November 21 @ 12:30 pm
525 Boyer Hall,, 611 Charles E Young Dr E,
Los Angeles, CA 90095
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W24: MERFISH/seqFISH

November 19 @ 1:30 pm - November 21 @ 4:30 pm
525 Boyer Hall,, 611 Charles E Young Dr E,
Los Angeles, CA 90095
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December 2019

W8: Variant Discovery with GATK

December 3 @ 9:30 am - December 5 @ 12:00 am
525 Boyer Hall,, 611 Charles E Young Dr E,
Los Angeles, CA 90095
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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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