Chapter title |
Statistical Modeling of Coverage in High-Throughput Data
|
---|---|
Chapter number | 4 |
Book title |
Deep Sequencing Data Analysis
|
Published in |
Methods in molecular biology, January 2013
|
DOI | 10.1007/978-1-62703-514-9_4 |
Pubmed ID | |
Book ISBNs |
978-1-62703-513-2, 978-1-62703-514-9
|
Authors |
David Golan, Saharon Rosset, Golan, David, Rosset, Saharon |
Abstract |
In high-throughput sequencing experiments, the number of reads mapping to a genomic region, also known as the "coverage" or "coverage depth," is often used as a proxy for the abundance of the underlying genomic region in the sample. The abundance, in turn, can be used for many purposes including calling SNPs, estimating the allele frequency in a pool of individuals, identifying copy number variations, and identifying differentially expressed shRNAs in shRNA-seq experiments.In this chapter we describe the fundamentals of statistical modeling of coverage depth and discuss the problems of estimation and inference in the relevant experimental scenarios. |
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