May 2013
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We will meet in Room 101B of the Flawn Academic Center (FAC) building. We STRONGLY encourage you to use the computers provided in the classroom, but you may also bring your personal laptops. |
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Resources tool list, file formats & more
Link to Etherpad: https://etherpad.mozilla.org/g2NxIEAFWL
Use this to post any questions you have about the lessons and tutorials.
Your Instructors
Name | Initials | Affiliation | Expertise | ||||
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SPHS | Director GSAF | Everything, if loosely defined (but especially | |||||
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 | ||||
Geoff Colburn Nichole Bennett | GC | Barrick Lab | Mappers, variant callers | Aaron Reba | AR NB | Parmesan/Singer Labs | Python, R, Unix |
Dan Deatherage | DD | Barrick Lab | TACC Unix, Python | ||||
Vinicio Reynoso | VR | Barrick Lab | Genome assembly |
, NGS Library Prep | |||
Nathan Abell | NA | Iyer Lab | Eukaryotes, RNA-Seq |
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Day 1a: Scott 1b: Jeff Instructors: meet 9am Monday for final check Each Part 1/Part 2 section needs to be standardized with: |
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Day 1: Linux/TACC Introduction and Read Mapping
Part 1: Linux/TACC Introduction
- General introduction (SPHS)
- Linux refresher (SPHS)
- Using TACC's Lonestar Cluster (SPHS/AR)
- Recap and "for further study"
Part 2: Read Mapping
- Introduction to next-gen sequencing technologies (SPHSJB)
- Application: Example genome variant calling pipeline (JB)
- Evaluating your raw sequencing data (JB/AB)
- Introduction to Mapping and Tutorial
- Tutorial - Start diploid mapping for Day 2
- Variant calling workflow diagram:
- (JB)
- Mapping tutorial (bowtie, BWA, bowtie2) (JB)
Enrichment modules (4:30-5:30)
- Sharing Linux tricks - linux one-liners (SPHS)
- Making it easier to work Working on TACC from a your Mac or PC (JB)
...
Extras
- Tutorial - Start diploid mapping for Day 2
- Running Unix & Perl for Biologists tutorial at TACC
- Installing Virtual machine & Linux on Windows (DP)
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Day 2: Handling Raw and Aligned sequences, and Calling Genome Variants
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Part 1. Handling Raw and Aligned sequences
- Overview and Resources
- Evaluating your raw sequencing data (AB)
- Mapped read data evaluation (SAMtools) (DP)
Part 2. Calling Genome Variants
Enrichment module (12:30-1:30)
- Installing Linux tools (JBShell Scripting (SPHS/AB)
Enrichment modules (4:30-5:30)
- Shell Scripting (SPHS/ABInstalling Linux tools (JB)
Extras
- Calling variants in diploid genomes (SPHS)
- Introduction to genome variation
- Variant calling with GATK (SPHS)
- Annotating variants (SPHS)
- (JB)
- Visualize mapped data at UCSC genome browser (AB)
- Mapped read data evaluation (SAMtools) (SPHS, DP)
- Genome variation in mixed samples (FreeBayes, deepSNV) (JB)
- Identifying structural variants (SVDetect) (JB)
- Practical advice - short read re-sequencing data
- SRA toolkit (AB)
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Day 3: RNA-seq
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Part 1. Introduction to RNA-seq Counting
Part 2. The Tuxedo RNA-seq Pipeline (Tophat & Cufflinks)
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Enrichment modules (4:30-5:30)
Extras
Extras
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Day 4: Assembly and Annotation
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Part 1. Genome Assembly
Part 2. Assembly Annotation
- Genome Annotation (Glimmer3) (VRSPHS)
- Evaluating & Visualizing assemblies (bacterial, SPHS)
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).
Enrichment module (4:30-5:30)
- Transcriptome assembly & annotation
- Protein functional classification...
- Custom Genome Databases
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