Command Line Unix: BLAST, RepeatMasker, Herne
PowerPoint presentation with instructions for running BLAST, RepeatMasker, and the BLAST output viewer Herne on the command-line.
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Lecture
Fulton Lecture Notes
The lecture notes from a presentation by Bob Fulton point out some of the more advanced features of Consed, the base caller phred, and the assembler phrap. This document should be read after students have some experience using Consed but before they begin working on their fosmids.
The D. grimshawi dot chromosome
This PowerPoint presentation explains our strategy, detailing the source of the raw sequence data for the D. grimshawi dot chromosome.
Overview of the Drosophila modENCODE Hybrid Assemblies
This PowerPoint presentation provides a general overview of the hybrid assemblies produced by the Baylor College of Medicine Human Genome Sequencing Center as part of the Drosophila modENCODE project. This presentation provides a brief introduction to the source of the raw sequence data and the protocol used by BCM-HGSC to construct the draft D. biarmipes genome assemblies.
The Genomics Education Partnership: Investigating the Evolution of the Dot Chromosome in Drosophila
This lecture by Dr. Sarah Elgin (Washington University in St. Louis) provides a general overview of the Genomics Education Partnership. It describes the current GEP research problem of identifying factors involved in heterochromatin formation and maintenance through comparative genomics in Drosophila.
RNA-Seq Primer
This PowerPoint presentation provides a brief introduction to the different types of RNA-Seq evidence tracks (e.g. Bowtie, TopHat, Cufflinks) that are on the GEP UCSC Genome Browser.
Common Annotation Errors
This PowerPoint presentation describes the common errors observed in student annotations.
UNIX for Consed
This PowerPoint presentation discusses the basic directory structure required by Consed and the UNIX commands used to launch Consed.
Gene Finding in Chimpanzee
A step-by-step tutorial that takes the student through a gene identification problem in a chimpanzee BAC sequence using predictions from a gene finder (Genscan), the UCSC Browser and BLAST.
Annotation of Drosophila Primer
This PowerPoint presentation provides a brief primer on the recommended annotation strategy for Drosophila projects. The presentation provides an overview of the goals of the GEP annotation project, an introduction to RNA-Seq, web databases, and a discussion on the phases of the splice donor and acceptor sites.
