Title: SSC Intro to NGS Bioinformatics Course  
Author: Scott Patrick Hunicke-Smith May 10, 2012
Last Changed by: Anna M Battenhouse May 23, 2013
Tiny Link: (useful for email) https://wikis.utexas.edu/x/dwQGAg
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Incoming Links
Core NGS Tools (6)
    Page: 2020 Piping and redirection
    Page: Piping and redirection
    Page: Linux fundamentals
    Page: 2020 Linux fundamentals
    Page: 2021 Linux fundamentals
    Page: 2022 Linux fundamentals
Introduction to Unix/Linux (1)
    Page: Some Linux commands
Bioinformatics Team (BioITeam) at the University of Texas (7)
    Page: Genome Variant Analysis Course 2016
    Page: Genome Variant Analysis Course 2015
    Page: Diagram of running a job on Lonestar
    Page: Mapping tutorial
    Page: Genome Variant Analysis Course 2014
    Page: Old Home page
    Page: Linux final
wikis.utexas.edu/display/CbbShortBashScript (1)
    Page: Linux Fundamentals
Hierarchy
Parent Page
    Page: Training
Children (48)
    Page: Lonestar Profile
    Page: Diagram of Lonestar's directories
    Page: Diagram of running a job on Lonestar
    Page: Evaluating your raw sequencing data
    Page: Mapping tutorial
    Page: Integrative Genomics Viewer (IGV) tutorial
    Page: Workflow diagram of variant calling
    Page: Getting started with Unix and Perl
    Page: Variant calling tutorial
    Page: Visualize mapped data at UCSC genome browser
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Recent Changes
Time Editor  
May 23, 2013 06:22 Anna M Battenhouse View Changes
Migrated to Confluence 5.3
May 23, 2013 06:22 Anna M Battenhouse View Changes
May 23, 2013 06:22 Anna M Battenhouse View Changes
Migrated to Confluence 4.0
May 23, 2013 06:22 Anna M Battenhouse View Changes
May 21, 2013 08:04 Nichole L Bennett  
Outgoing Links
External Links (10)
    www.youtube.com/watch?v=45vNetkGspo&feature=player_detailpa…
    www.hindawi.com/journals/bmri/2012/251364/
    https://etherpad.mozilla.org/g2NxIEAFWL
    www.youtube.com/watch?v=77r5p8IBwJk
    https://wikis.utexas.edu/display/GSAF/About+Us#Scott
    https://wikis.utexas.edu/display/GSAF/Illumina+-+all+flavor…
    barricklab.org
    prezi.com/hi5qbnt5uio_/an-introduction-to-bioinformatics/?a…
    www.broadinstitute.org/scientific-community/science/platfor…
    www.utexas.edu/maps/main/buildings/fac.html
Bioinformatics Team (BioITeam) at the University of Texas (50)     Page: Shell Script
    Page: Installing Linux tools
    Page: Transcriptome assembly & annotation
    Page: Evaluating & Visualizing assemblies
    Page: Visualize mapped data at UCSC genome browser
    Page: Getting started with Unix and Perl
    Page: Tutorial - Start diploid mapping for Day 2
    Page: Exercises
    Page: Variant calling tutorial
    Page: non-coding RNA analysis
    Page: Editing files
    Page: Linux start
    Page: Variant calling with GATK
    Page: Mapping tutorial
    Page: SSC Intro to NGS Bioinformatics Course
    Page: Differential gene expression analysis
    Page: Evaluating your raw sequencing data
    Page: Genome Assembly
    Page: SRA toolkit
    Page: Custom Genome Databases
    Page: Genome variation in mixed samples (FreeBayes, deepSNV)
    Page: NGS Course Resources
    Page: Calling variants in diploid or multiploid genomes
    Page: Diagram of Lonestar's directories
    Page: General introduction
    Page: Key take home points
    Page: As you're getting settled
    Page: Example BWA alignment script
    Page: Lonestar Profile
    Page: Start tophat by submitting to lonestar
    Page: Practical advice - short read re-sequencing data
    Page: Differential expression with splice variant analysis aug2012
    Page: Identifying mutations in microbial genomes (breseq)
    Page: Workflow diagram of variant calling
    Page: Genome Assembly (velvet)
    Page: Scott's list of linux one-liners
    Page: Linux refresher
    Page: Annotating Variants
    Page: Introduction to genome variation
    Page: Genome Annotation (Glimmer3)
    Page: Linux final
    Page: Handling Sequences Overview
    Page: instructor action item list
    Page: Identifying structural variants (SVDetect)
    Page: Mapped read data evaluation (SAMtools)
    Page: Integrative Genomics Viewer (IGV) tutorial
    Page: Using SFTP for file browsing on Linux.
    Page: Installing Virtual machine & Linux on Windows
    Page: Recap and "for further study"
    Page: Diagram of running a job on Lonestar