All Tutorials

  • Fri Dec 12, 1:00 pm - 2:30 pm
    138
    Cargill Building

    This tutorial is part of the MPGI/MSI PacBio workshop being held on December 10, 2014. Separate registration for the entire event is required. See the description of the event and link to the registration form on the MSI website.


    Recent advances in long read sequencing have revolutionized genome assembly, enabling complete reconstruction of microbial genomes and significantly improved assemblies for higher organisms. This interactive tutorial introduces open source tools and workflows for analyzing, assembling, and interpreting Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing data. The workshop will primarily focus on PacBio’s SMRT Analysis graphical user interface (to be fully supported by MSI), but other command line tools for correction, assembly, and polishing of PacBio data will also be briefly introduced.


    Topics covered will include managing and importing raw SMRT cell data, adapter removal and subread filtering, SMRT cell loading and quality control, read self-correction and pre-assembly, de novo long read assembly with the hierarchical genome assembly process (HGAP), assembly polishing with Quiver, and base modification and methylation motif detection.


    Basic familiarity with the Unix command line is beneficial but not required. Example data will be provided, but attendees will have the opportunity to analyze their own PacBio data if available.


  • Wed Dec 10, 2:30 pm - 3:30 pm
    138
    Cargill Building

    This tutorial is part of the MPGI/MSI PacBio workshop being held on December 10, 2014. Separate registration for the entire event is required. See the description of the event and link to the registration form on the MSI website.


    Recent advances in long read sequencing have revolutionized genome assembly, enabling complete reconstruction of microbial genomes and significantly improved assemblies for higher organisms. This interactive tutorial introduces open source tools and workflows for analyzing, assembling, and interpreting Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing data. The workshop will primarily focus on PacBio’s SMRT Analysis graphical user interface (to be fully supported by MSI), but other command line tools for correction, assembly, and polishing of PacBio data will also be briefly introduced.


    Topics covered will include managing and importing raw SMRT cell data, adapter removal and subread filtering, SMRT cell loading and quality control, read self-correction and pre-assembly, de novo long read assembly with the hierarchical genome assembly process (HGAP), assembly polishing with Quiver, and base modification and methylation motif detection.


    Basic familiarity with the Unix command line is beneficial but not required. Example data will be provided, but attendees will have the opportunity to analyze their own PacBio data if available.


  • Thu Oct 23, 2:00 pm - 5:00 pm
    404
    Walter Library

    This tutorial is paired with Analyzing ChIP-Seq Data using Galaxy and will take the user though the same steps but, using the command line versions of the tools used in the Galaxy environment. 


    This tutorial will:


    1. Provide a brief introduction to MSI systems.
    2. Provide a very brief introduction to UNIX.
    3. Take users step-by-step though the process needed to analyze ChIP-Seq data
    4. Provide users with a basic PBS script to automate the mapping and peak calling.
    5. Teach users how to edit and run the script to be used in the future. 


    Students will need to bring their own laptops to this tutorial and have some software preinstalled. Once you sign up for the tutorial, instructions for which software to have installed will be given to you.


  • Tue Oct 21, 2:00 pm - 5:00 pm
    575
    Walter Library

    This practical, hands-on tutorial is designed to give participants experience with ChIP-Seq data analysis using the Galaxy platform. The analysis in this tutorial is typical of experiments using ChIP-Seq data to identify transcription factor binding sites in eukaryotic, high quality genomes. 


  • Thu Oct 16, 10:00 am - 12:00 pm
    402
    Walter Library

    This lecture will go over the basics of ChIP-Seq experimental design and analysis. 


    Lecture Topics:


    • ChIP-seq for transcription factor vs chromatin

    • Experimental design, replicates and controls

    • Peak calling algorithms 

    • Outside data repositories 

    • Interacting with your data

  • Tue Oct 14, 2:00 pm - 5:00 pm
    138
    Cargill Building
    This is a practical, hands-on tutorial designed to give participants experience with RNA-Seq data

    analysis using Tophat and Cufflinks in Galaxy. The analysis in this tutorial is typical of

    experiments in plant species with adequate quality genomes and genome annotation.

    Participants are expected to be familiar with next-generation sequence data and basic theory of

    RNA-Seq. Participants do not need previous experience with Tophat, Cufflinks, or Galaxy

  • Thu Oct 9, 2:00 pm - 5:00 pm
    138
    Cargill Building

    This hands-on tutorial will help a new user understand how to use the Galaxy platform to analyze NGS data by working though the quality control steps needed for Illumina sequencing data. 


    This tutorial will:


    1. Introduce the Galaxy platform to new users


    2. Explain the features of the Galaxy platform including:
          a. Data libraries
          b. Histories
          c. Workflows
          d. Getting Help


    3. Take users though the specific quality control and trimming steps needed to work with Illumina sequencing data


  • Thu Oct 2, 2:00 pm - 5:00 pm
    575
    Walter Library
    This is a practical, hands-on tutorial designed to give participants experience with RNA-Seq

    data analysis using Tophat, Cufflinks, and CummRbund in Galaxy. The analysis in this

    tutorial is typical of experiments in eukaryotic species with high-quality genomes and

    genome annotation available. Participants are expected to be familiar with next-generation

    sequence data, basic theory of RNA-Seq, and Galaxy. Participants do not need previous

    experience with Tophat, Cufflinks, or CummeRbund.

  • Tue Sep 30, 1:00 pm - 3:00 pm
    575
    Walter Library

    This tutorial is for new MSI users and interested individuals, and it provides an introduction to the facilities and computational resources at MSI. The quick start portion of the tutorial consists of instructions for setting up accounts, and accessing the various machines and resources. The second portion consists of a brief introduction to the MSI Linux environment, including hands-on examples. The UNIX operating system is a fundamental part of the MSI experience for people using the MSI Linux workstations and core systems. Many of MSI's scientific codes require that the user understand basic UNIX operating commands and functionality. This latter part of the tutorial will give a novice user an introduction to using the UNIX operating environment to navigate and use MSI resources.


  • Thu Sep 25, 1:00 pm - 3:00 pm
    105
    Cargill Building

    This lecture will go over more advanced RNA-Seq topics and complements Basics of RNA-seq. 


    Lecture Topics:


    • Non-mammal specific RNA-Seq issues

    • Transcriptome assembly and other uses of RNA-Seq data

    • Sample replicate and pooling decisions

    • Advanced mapping statistics and troubleshooting 

    • Exploring the data and results from a DGE experiment

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