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 |