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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
Use this to post any questions you have about the lessons and tutorials.
Your Instructors
Name | Initials | Affiliation | Expertise |
|---|---|---|---|
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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- Introduction to next-gen sequencing technologies (JB)
- Variant calling workflow diagram:
- (JB)
- Mapping tutorial (bowtie, BWA, bowtie2) (JB)
- Integrative Genomics Viewer (IGV) tutorial (JB)
- Tutorial - Start diploid mapping for Day 2
Enrichment modules (4:30-5:30)
- Sharing Linux tricks - linux one-liners (SPHS)
- Working on TACC from your Mac or PC (AB)
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:
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Handling Raw and Aligned sequences, and Calling Genome Variants
Part 1.
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Handling Raw and Aligned sequences
- Overview and Resources
- Evaluating your raw sequencing data (DP/AB)
- Mapped read data evaluation (SAMtools) (DP/AB)
- Practical advice - Final odds & ends for short read re-sequencing data
Part 2. Calling Genome Variants
- Example genome variant calling pipeline (SPHS (JB)
- Introduction to genome variation
- (SPHS)
- Variant calling tutorial (SAMtools) (SPHSJB)Calling variants in diploid genomes (SPHS
- Integrative Genomics Viewer (IGV) tutorial (JB)
Enrichment module (12:30-1:30)
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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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- Genome Annotation (Glimmer3) (VRSPHS)
- Evaluating & Visualizing assemblies (bacterial, SPHS)
Enrichment module (12:30-1:30)
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