All Tutorials

  • Thu Apr 9, 9:00 am - 11:30 am
    138
    Cargill Building

    This tutorial is part of the MSI/NSF Long-read assembly workshop being held on April 9, 2015. 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.


  • Fri Apr 3, 1:00 pm - 3:00 pm
    575
    Walter Library

    Progenesis QI staff will give a hands-on tutorial demonstrating Progenesis QI's analysis capabilities. 


  • Fri Apr 3, 9:00 am - 12:00 pm

    Staff from Progenesis QI will give an overview of what Progenesis QI can do, what is new in version 2 and to answer your questions. 


    Morning Lecture will be in Mayo 3-125
    Afternoon Hands-on will be in Walter Library 575


    Schedule:
    9:00 am registration 
    9:30 am introduction
    9:45 am Progenesis QI overview and what’s new in Version 2
    10:00 – 11:50 am Progenesis QI operational overview with questions
    12:00 pm Lunch on the 5th floor of Walter Library
    1:00 – 3:30 pm hands on demonstration in Walter Library 575


  • Thu Mar 19, 1:30 pm - 4:30 pm
    138
    Cargill Building

    -


  • Tue Jan 13, 10:00 am - 11:30 am
    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 Jan 7, 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 17, 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.


  • 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.


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