Schatz Laboratory - Teaching

Teaching

2017

JHU Applied Comparative Genomics

2016

JHU CS 600.226 Data Structures

2015

CSHL Genome Access

Quantitative Biology & Bioinformatics

Special Topics

Exercises

Beyond the Genome Challenges

BTG11: Viral Insertion Identify the virus in a cancer exome sequencing project

BTG12: Digital Encoding Identify the secret message inserted into a microbial genome

BTG13: Metagenomics Variants Identify the secret message encoded as variants within a metagenomics sample

Genomics

Read Mapping Read mapping, identifying variants, running BWA/SAMTools

RNA-seq Analysis Read mapping, computing expression, running Bowtie/Tophat/Cufflinks

Genome assembly De novo assembly and error correction, whole genome alignment

Coverage analysis Coverage analysis using plane-sweep algorithms

Probability and Statistics

Rolling a die Uniform Random Probability

Flipping a coin Binimal and Normal Distributions

Marbles in jars Poisson Distribution

Throwing darts Exponential Distribution

Computing

Python Basics 1 Introduction to python, variables, lists, conditions, loops

Python Basics 2 Brute force search, dictionaries, motif finding

Hadoop Getting started with Hadoop, kmer counting and word analysis

Essential Resoures

Online Resources

NCBI PubMed, Genomes, Genbank, SRA

UCSC Genome Browser Interactive genome plots, coverage, annotations

Galaxy Interactive genome analysis (CSHL version)

SeqAnswers Forums and tutorials for genomics analysis

Khan Academy Videos and Tutorials on many science and mathematics related topics

CiteULike Social networking for citations and papers

Rosalind Programming and Bioinformatics exercises

JHU Comp Genomics iPython Notebooks of basic string algorithms

FASTQ trimming and error correction

FASTX-Tools Filter and trim fastq files

Quake Error Correction of Short Reads

Aligners and variant callers

Bowtie/Bowtie2 Ultra-fast short read mapping with the BWT

BWA Feature rich short read alignment

SAMTools SAM/BAM alignment filtering and scoring

Picard SAM/BAM alignment filtering

BedTools Slice and dice genomics intervals

GATK Variant calling

Hydra Structural Variations calling with discordant pair analysis

RNA-seq Analysis

TopHat Spliced alignment for RNA-seq

Cufflinks Transcript assembly and quantification

Trinity De novo transcript assembly and quantification

Assembly and Whole Genome Alignment

ALLPATHS-LG Assembly of short reads

SOAPdenovo Assembly of short reads

Celera Assembler Assembly of long reads

MUMmer Whole Genome Alignment

AMOS Assembly and assembly related tools

Statistics and Visualization

Canopy Python Integrated Development Environment

matplotlib Visualization in python

R Statistics and visualization

Circos Circular plots of genomes and other data

Graphviz Layout and render graphs

Weka Data Mining and classification

IGV Interactive Genomics Viewer for short reads

Last Updated: Mar 31 2017 11:24:55 AM