Springer Protocols: Abstract: 9. Extraction and Annotation of SAGE Tags Using Sequence Quality Values

9. Extraction and Annotation of SAGE Tags Using Sequence Quality Values

By: Jeppe Emmersen²

Abstract

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Data analysis of serial analysis of gene expression (SAGE) tag experiments begins with the extraction of tags from single-pass sequence files of ditag concatemers. When using DNA base quality values generated during base calling, it is possible to control the false-positive discovery rate of unique tags. This chapter describes how to set up a system for generating tag lists from quality associated sequence data.

Affiliation(s): (2) Department of Biochemistry, Chemistry, and Environmental Engineering, University of Aalborg, Aalborg, Denmark

Book Title: Serial Analysis of Gene Expression (SAGE): Methods and Protocols

Series: Methods in Molecular Biology | Volume: 387 | Pub. Date: Jun-05-2007 | Page Range: 123-132 | DOI: 10.1007/978-1-59745-454-4_9

Subject: Genetics/Genomics

Key Words: Phred - quality values - mapping - sequence databases - UniGene.

References

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