Genomics 6203

Genomics 6203

This is the general syllabus for BINF 6203 — Genomics.

Since genomics technologies and analysis methods change rapidly, we do not typically assign a textbook for the course, relying instead on recent review articles to cover important parts of the Genomics domain. If you would like to have a book that provides an overview in addition to the assigned readings, one possibility is Introduction to Genomics, by Arthur Lesk. It does not align perfectly with the course content but it does provide a reasonable overview of many course topics.

1Introduction to GenomicsGenomic Data Repositories — Genbank and SRA
Lab 1: SRA access and file conversion
2Genomic Data Formats and VisualizationNext Gen Sequencing Platforms
3NGS Data QC
Lab 2: FastQC, Fast-X and Trimmomatic
Ab initio genome assembly
4NGS assembly algorithms
Lab 3: de novo assembly with SPAdes
Approaches to whole genome sequencing
5Reference-based “assembly”
Lab 3: reference-based mapping with bowtie2/samtools/etc
Read-mapping algorithms
6Genome annotation
Lab 5: gene annotation with myRAST
Genefinding Algorithms
7Annotation formats and track manipulation
Lab 6: Genome Browsers and Bedtools
8Comparative Genomics


Gene Ontology and functional classifications
7Orthology; content and functional comparison
Lab 7: Genome alignment and comparison
Variant calling
8Human genome variation projects Lab 8: Basic variant calling out of genome dataHaplotyping and linkage disequilibrium
9Whole Genome association studiesDifferential expression analysis
Lab 9: RNA-Seq with a reference genome
10Manipulating transcriptome dataData normalization
Lab 10: RNA-Seq analysis by transcriptome assembly
11Statistics for gene expression analysisPathway and gene set analysis
Lab 11: GAGE and Pathview
12PathviewGene regulation
Lab 12: ChIP-Seq analysis in CLC Genomics
13Current topicsCurrent topics

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