BINF 6203: Genomics

BINF 6203: Genomics

This is the game plan for BINF 6203 — Genomics in Spring Semester 2015. Class times: 11:00-12:15 MW Lab: 12:15-2:00 M

Links to these posts will also be provided in Moodle, but this post will serve as a directory for the course. Links will go live as the tutorials are ready.

The recommended textbook is Next-Generation DNA Sequencing Informatics, by Stuart Brown. This book offers an overview of the topics presented in the course and will be supplemented by current research papers.

Week Monday Wednesday
January 5-7 Introduction to Genomics
January 12-14 Genomic Data Repositories — Genbank and SRA
Lab 1: SRA access and file conversion
Genomic Data Formats and Visualization
January 19-21 Martin Luther King Day Next Gen Sequencing Platforms
January 26-28 NGS Data QC
Lab 2: FastQC, Fast-X and Trimmomatic
Ab initio genome assembly
February 2-4 NGS assembly algorithms
Lab 3: de novo assembly with SPAdes
Approaches to genome sequencing
February 9-11 Reference-based “assembly”
Lab 3: reference-based mapping with bowtie2/samtools/etc
Read-mapping algorithms
February 16-18 Genome annotation
Lab 5: gene annotation with myRAST
SNOW DAY
February 23-25 Genefinding Algorithms MIDTERM EXAM
March 9-11 Annotation formats and track manipulation
Lab 6: Genome Browsers and Bedtools
Gene Ontology and functional classifications
March 16-18 Comparative Genomics
Lab 7: Genome alignment and comparison
Orthology; content and functional comparison
March 23-25 Variant calling
Lab 8: Basic variant calling out of genome data
Human genome variation projects
March 30-April 1 Haplotyping and linkage disequilibrium
Lab 8 + catch up week
Whole Genome association studies
April 6-8 Differential expression analysis
Lab: RNA-Seq analysis in CLC Genomics
Manipulating transcriptome data
April 13-15 Data normalization
Lab: RNA-Seq analysis with command line pipelines
Statistics for gene expression analysis
April 20-22 Pathway and gene set analysis
Lab: GAGE
Pathview
April 27 Gene regulation
ChIP-Seq analysis in CLC Genomics
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