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May
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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. |
| Table of Contents |
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Resources tool list, file formats & more
Link to Etherpad: https://etherpad.mozilla.org/g2NxIEAFWL
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Use
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this
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to
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post
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any
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questions
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you
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have
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about
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the
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lessons
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and
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tutorials.
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Your
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Instructors
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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 |
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 |
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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)
- Recap and "for further study"
Part 2: Read Mapping
- Introduction to next-gen sequencing technologies (JB)
- Variant calling workflow diagram:
- (JB)
- Mapping tutorial (bowtie, BWA, bowtie2) (JB)
Enrichment modules (4:30-5:30)
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- (SPHS)
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- Working
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- on
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- TACC
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- from
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- your
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- Mac
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- or
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- PC
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- (AB)
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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
Part 1. Handling Raw and Aligned sequences
- Overview and Resources
- Evaluating your raw sequencing data (AB)
- Mapped read data evaluation (SAMtools) (DP)
Wiki Markup {hidden-data} * [Practical advice - Final odds & ends for short read re-sequencing data|Practical advice - short read re-sequencing data] {hidden-data}
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Part
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2.
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Calling
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Genome
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Variants
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- Variant
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- calling
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- workflow
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Enrichment module (12:30-1:30)
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- (SPHS/AB)
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Enrichment
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modules
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(4:30-5:30)
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- (JB)
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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)
- Genome variation in mixed samples (FreeBayes, deepSNV) (JB)
- Identifying structural variants (SVDetect) (JB)
- SRA toolkit (AB)
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Day 3: RNA-seq
Part 1. Introduction to RNA-seq Counting
Part 2. The Tuxedo RNA-seq Pipeline (Tophat & Cufflinks)
Enrichment module (12:30-1:30)
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- (
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- JB)
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Enrichment
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modules
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(4:30-5:30)
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- (DA)
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Extras
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Day 4: Assembly and Annotation
Part 1. Genome Assembly
Part 2. Assembly Annotation
- Genome Annotation (Glimmer3) (SPHS)
- Evaluating & Visualizing assemblies (bacterial, SPHS)
Enrichment module (12:30-1:30)
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- Office
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- hours:
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- "I
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- want
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- to
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- learn
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- how
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- to
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- install
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- and
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- use
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- this
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- tool
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- called
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- _____
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- _
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- that
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- we
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- didn't
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- talk
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- about
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- in
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- class."
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- (JB).
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Enrichment
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module
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(4:30-5:30)
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- Protein
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- functional
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- classification...
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Resources
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