Setting CAGE tags in a genomic context

Faulkner, G. J. and Grimmond, S. M. (2009). Setting CAGE tags in a genomic context. In Cap- Analysis Gene Expression (Cage): The Science of Decoding Gene Transcription (pp. 93-100) Singapore: Pan Stanford Publishing. doi:10.4032/9789814241359

Author Faulkner, G. J.
Grimmond, S. M.
Title of chapter Setting CAGE tags in a genomic context
Title of book Cap- Analysis Gene Expression (Cage): The Science of Decoding Gene Transcription
Place of Publication Singapore
Publisher Pan Stanford Publishing
Publication Year 2009
Sub-type Other
DOI 10.4032/9789814241359
Open Access Status
Year available 2009
ISBN 9789814241342
Chapter number 8
Start page 93
End page 100
Total pages 8
Total chapters 17
Collection year 2010
Language eng
Subjects 1300 Biochemistry, Genetics and Molecular Biology
Abstract/Summary The detection and quantification of transcriptional activity on the genome by CAGE requires reliable and high-throughput tag mapping. Here, we discuss the basic considerations of sequence tag mapping and how these apply to CAGE. The current CAGE mapping pipeline is then described in detail, in particular how it has been updated to utilize iterative global exact matching for each tag rather than heuristic algorithm local alignment. Combined with the addition of a novel method to resolve tags that map to multiple genomic locations, the most recent evolution of the CAGE mapping pipeline is faster, more accurate and provides better coverage than the previous approach, as we demonstrate using a sample CAGE library. Finally, the pipeline is easily customized for other sequence tag technologies, suggesting broad utility in the era of next-generation sequencing.
Q-Index Code BX
Q-Index Status Provisional Code
Institutional Status Non-UQ

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