Page Comparison

h1. May 2013

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We will meet in Room 101B of the [Flawn Academic Center (FAC) building|http://www.utexas.edu/maps/main/buildings/fac.html].  We STRONGLY encourage you to use the computers provided in the classroom, but you may also bring your personal laptops.
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{toc}
*[Resources tool list, file formats & more|NGS Course Resources]*

Link to Etherpad: [https://etherpad.mozilla.org/g2NxIEAFWL]


Use this to post any questions you have about the lessons and tutorials.

h2. Your Instructors

|| Name || Initials || Affiliation || Expertise ||
| [Scott Hunicke-Smith|https://wikis.utexas.edu/display/GSAF/About+Us#Scott] | SPHS | Director GSAF | Everything, if loosely defined (but especially {{awk}}) |
| [Jeff Barrick|http://barricklab.org] | JB | Asst. Prof. Biochemistry | Microbes, Perl, C++, Mac, miscellanea |
| Dhivya Arasappan (_in absentia_) | DA | GSAF | RNA-seq, transcriptome assembly |
| Anna Battenhouse | AB | Iyer Lab | Eukaryotes, Bash scripting, UCSC Genome Browser |
| Daechan Park | DP | Iyer Lab | Eukaryotes, ChIP-seq, Python, Samtools \\ |
| Nichole Bennett | NB | Parmesan/Singer Labs | Python, R, Unix \\ |
| Dan Deatherage | DD | Barrick Lab | Unix, Python, NGS Library Prep |
| Nathan Abell | NA | Iyer Lab | Eukaryotes, RNA-Seq |

[instructor action item list]




{expand:Info for the instructors}
Day 1a: Scott 1b: Jeff
Day 2a: Jeff, Daechan, Anna, 2b: Scott
Day 3a: Jeff 3b: Iyer lab
Day 4a: Jeff, 4b: Scott

Instructors: meet 9am Monday for final check

Each Part 1/Part 2 section needs to be standardized with:
\*Learning Objectives
\*Theory
\*Workflow diagram (data, toolbox/recipe, exercises)
\*Tutorial (bulk of time here)
\*Recap learning objectives
\*Next steps...
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{anchor:day1}

h2. Day 1: Linux/TACC Introduction and Read Mapping

h3. Part 1: Linux/TACC Introduction

* [General introduction] (SPHS)
** [Introduction to Bioinformatics Prezi|http://prezi.com/hi5qbnt5uio_/an-introduction-to-bioinformatics/?auth_key=499992bd5a55dad39717693f9d523f9073bd4693]
* [Linux refresher|Linux refresher] (SPHS)
** [Step 1: Start somewhere|Linux start]
** [Step 2: Establishing a profile on Lonestar|Lonestar Profile]
** [Step 3: Editing files|Editing files]
** [Step 4: Final explanations|Linux final]
** [!pdf_icon.gif! Unix command cheat sheet|^UnixCommandCheatSheet.pdf]
* [Using TACC's Lonestar Cluster] (SPHS)
** [Diagram of Lonestar's directories]
** [!pdf_icon.gif! Lonestar cheat sheet|bioiteam:SSC Intro to NGS Bioinformatics Course^LonestarCheatSheet.pdf]
** [Diagram of running a job on Lonestar]
** [!pdf_icon.gif! Launcher Creator cheat sheet|bioiteam:SSC Intro to NGS Bioinformatics Course^LauncherCreatorCheatSheet.pdf]
** [Using SFTP for file browsing on Linux.]
* [Recap and "for further study"]

h3. Part 2: Read Mapping

* Introduction to next-gen sequencing technologies (JB)
** [Paper comparing NGS technologies (Liu et al., 2012)|http://www.hindawi.com/journals/bmri/2012/251364/]
** [Official Illumina video|http://www.youtube.com/watch?v=45vNetkGspo&feature=player_detailpage#t=191s] \| [Another Illumina video|http://www.youtube.com/watch?v=77r5p8IBwJk]
** [Broad Center GA Boot Camp|http://www.broadinstitute.org/scientific-community/science/platforms/genome-sequencing/broadillumina-genome-analyzer-boot-camp]
* Variant calling workflow diagram: [!png_icon.gif! Overview|Workflow diagram of variant calling] [!pdf_icon.gif! Detailed|^VariantCallingWorkflowMay2013.pdf]
* [!pdf_icon.gif! Introduction to mapping presentation|^Barrick_IntroToMapping.pdf] (JB)
* [Mapping tutorial (bowtie, BWA, bowtie2)|Mapping tutorial] (JB)

h4. Enrichment modules (4:30-5:30)

* [Sharing Linux tricks - linux one-liners|Scott's list of linux one-liners] (SPHS)
* Working on TACC from your Mac or PC (AB)
** [Editing files, more detail|Editing files]

h4. Extras

* [Tutorial - Start diploid mapping for Day 2|Tutorial - Start diploid mapping for Day 2]
* [Running _Unix & Perl for Biologists_ tutorial at TACC|Getting started with Unix and Perl]
* [Installing Virtual machine & Linux on Windows] (DP)

{anchor:day2}

h2. Day 2: Handling Raw and Aligned sequences, and Calling Genome Variants

h3. Part 1. Handling Raw and Aligned sequences

* [Overview and Resources|Handling Sequences Overview]
* [Evaluating your raw sequencing data] (AB)
** [GSAF adaptor and barcode sequence resource|https://wikis.utexas.edu/display/GSAF/Illumina+-+all+flavors]
* [Mapped read data evaluation (SAMtools)|Mapped read data evaluation (SAMtools)] (DP)
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* [Practical advice - Final odds & ends for short read re-sequencing data|Practical advice - short read re-sequencing data]
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h3. Part 2. Calling Genome Variants

* [!pdf_icon.gif! Introduction to variant calling presentation|^Barrick_IntroToVariantCalling.pdf] (JB)
** Variant calling workflow diagram: [!png_icon.gif! Overview|Workflow diagram of variant calling] [!pdf_icon.gif! Detailed|^VariantCallingWorkflowMay2013.pdf]
* [Variant calling tutorial (SAMtools)|Variant calling tutorial] (JB)
* [Integrative Genomics Viewer (IGV) tutorial|Integrative Genomics Viewer (IGV) tutorial] (JB)

h4. Enrichment module (12:30-1:30)

* [Shell Scripting|Shell Script] (SPHS/AB)

h4. Enrichment modules (4:30-5:30)

* [Installing Linux tools] (JB)

h4. Extras

* [Calling variants in diploid genomes|Calling variants in diploid or multiploid genomes] (SPHS)
* [Introduction to genome variation]
* [Variant calling with GATK] (SPHS)
* [Annotating variants|Annotating Variants] (SPHS)
* [!pdf_icon.gif! Advanced genome variant calling presentation|^Barrick_AdvancedVariantCalling.pdf] (JB)
* [Visualize mapped data at UCSC genome browser|Visualize mapped data at UCSC genome browser] (AB)
* [Genome variation in mixed samples (FreeBayes, deepSNV)|Genome variation in mixed samples (FreeBayes, deepSNV)] (JB)
* [Identifying structural variants (SVDetect)|Identifying structural variants (SVDetect)] (JB)
* [SRA toolkit|SRA toolkit] (AB)

{anchor:day3}

h2. Day 3: RNA-seq

h3. Part 1. Introduction to RNA-seq Counting

* [!pdf_icon.gif! Introduction to RNA-seq|bioiteam:SSC Intro to NGS Bioinformatics Course^RNA-seq 15Aug12.pdf]
* [Differential gene expression analysis] (JB)

h3. Part 2. The Tuxedo RNA-seq Pipeline (Tophat & Cufflinks)

* [Differential expression with splice variant analysis|Differential expression with splice variant analysis aug2012]

h4. Enrichment module (12:30-1:30)

* [Identifying mutations in microbial genomes (breseq)|Identifying mutations in microbial genomes (breseq)] (JB)

h4. Enrichment modules (4:30-5:30)

* [Start tophat by submitting to lonestar|Start tophat by submitting to lonestar] (DA)

h4. Extras

* [Visualize mapped data at UCSC genome browser|Visualize mapped data at UCSC genome browser] (AB)
* [non-coding RNA analysis|non-coding RNA analysis]

{anchor:day4}

h2. Day 4: Assembly and Annotation

h3. Part 1. Genome Assembly

* [!ppt_icon.gif! Introduction to genome assembly|bioiteam:SSC Intro to NGS Bioinformatics Course^Assembly notes 15Aug12.pdf]
* [Genome Assembly Examples|Genome Assembly] (SPHS)
* [Tutorial: Genome Assembly (velvet)|Genome Assembly (velvet)] (SPHS)

h3. Part 2. Assembly Annotation

* [Genome Annotation (Glimmer3)|Genome Annotation (Glimmer3)] (SPHS)
* [Evaluating & Visualizing assemblies] (bacterial, SPHS)

h4. Enrichment module (12:30-1:30)

* Office hours: "I want to learn how to install and use this tool called \_____\_ that we didn't talk about in class." (JB).

h4. Enrichment module (4:30-5:30)

* [Transcriptome assembly & annotation]
* Protein functional classification...
* [Custom Genome Databases]

h2. Resources

* [Scott's list of linux one-liners|Scott's list of linux one-liners]
* [Example BWA alignment script]
* [Exercises]
* [Key take home points]

h4.* [Resources tool list, file formats & more|NGS Course Resources]

[As you're getting settled]