Sequencing depth and coverage: key considerations in genomic analyses

被引：896

作者：

Sims, David ^{[1
]}

Sudbery, Ian ^{[1
]}

Ilott, Nicholas E. ^{[1
]}

Heger, Andreas ^{[1
]}

Ponting, Chris P. ^{[1
]}

机构：

[1] Univ Oxford, Computat Genom Anal & Training Programme, MRC, Funct Genom Unit,Dept Physiol Anat & Genet, Oxford OX1 3PT, England

来源：

NATURE REVIEWS GENETICS | 2014年 / 15卷 / 02期

基金：

英国医学研究理事会;

关键词：

COPY-NUMBER VARIATION; DIFFERENTIAL EXPRESSION ANALYSIS; RNA-SEQ; GENE-EXPRESSION; CHROMATIN; REVEALS; ORGANIZATION; LANDSCAPE; DISCOVERY; BINDING;

D O I：

10.1038/nrg3642

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Sequencing technologies have placed a wide range of genomic analyses within the capabilities of many laboratories. However, sequencing costs often set limits to the amount of sequences that can be generated and, consequently, the biological outcomes that can be achieved from an experimental design. In this Review, we discuss the issue of sequencing depth in the design of next-generation sequencing experiments. We review current guidelines and precedents on the issue of coverage, as well as their underlying considerations, for four major study designs, which include de novo genome sequencing, genome resequencing, transcriptome sequencing and genomic location analyses (for example, chromatin immunoprecipitation followed by sequencing (ChIP-seq) and chromosome conformation capture (3C)).

引用

页码：121 / 132

页数：12

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