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h1. May 2013 {warning} 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. {warning} {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... {expand} {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) {hidden-data} * [Practical advice - Final odds & ends for short read re-sequencing data|Practical advice - short read re-sequencing data] {hidden-data} 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] |
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