Annotation Unix Worksheet
Exercise that uses UNIX tools (command-line BLAST and RepeatMasker) for gene annotations.
Exercise that uses UNIX tools (command-line BLAST and RepeatMasker) for gene annotations.
A simple exercise on using simple Unix commands to navigate to different directories and manipulate files.
A Unix reference sheet for commonly used Unix commands.
PowerPoint presentation with instructions for running BLAST, RepeatMasker, and the BLAST output viewer Herne on the command-line.
This PowerPoint presentation describes the common errors observed in student finishing projects.
All GEP projects are completed at least twice independently by GEP students. This document describes how to check two or more submissions of a finishing project for congruence. Ordinarily this is done centrally at Washington University, but in some cases may be of interest at a given school.
This document illustrates some of the advantages and potential problems with the BigDye and dGTP chemistries.
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.
One of the main tools used to verify the correctness of a genome assembly is comparison of an in-silico restriction digest to the real restriction digest data generated by the WU Genome Center. This document also covers how students can use the restriction digest data early in the assembly process to determine the number of copies of repeats in a given cluster or to estimate gap sizes.
Students can practice using Consed by working on a mouse contig. This exercise poses various challenges that students may encounter when working on their own projects.