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Primer Design

Calling Additional Reads

Students will typically need to request additional sequencing reactions in order to improve the quality of an assembly. This document describes some of the key considerations that students should keep in mind when they design oligonucleotide primers.

PCR Primer Selection Guide

This document contains advice on the factors that students should consider when designing PCR primers to resolve gaps and low quality regions. The document also includes the specific search parameters students should use to minimize the chance of off-target priming when designing PCR primers.

Drosophila Finishing Problem Set

Students can practice using Consed by working on two Drosophila projects. This exercise poses various challenges that students may encounter when working on their own projects.

Using Consed Graphically

A training document similar to “An Introduction to Consed,” this document contains a more detailed walkthrough that explores additional functions available in Consed.