不同组学研究建议采用的测序策略

Panda姐

https://genohub.com/recommended-sequencing-coverage-by-application/Table 1: Coverage and Read Recommendations by Application

Category	Detection or Application	Recommended Coverage (x) or Reads (millions)	References
Whole genome sequencing	Homozygous SNVs	15x	Bentley et al., 2008
	Heterozygous SNVs	33x	Bentley et al., 2008
	INDELs	60x	Feng et al., 2014
	Genotype calls	35x	Ajay et al., 2011
	CNV	1-8x	Xie et al., 2009; Medvedev at al., 2010
Whole exome sequencing	Homozygous SNVs	100x (3x local depth)	Clark et al., 2011; Meynert et al., 2013
	Heterozygous SNVs	100x (13x local depth)	Clark et al., 2011; Meynert et al., 2013
	INDELs	not recommended	Feng et al., 2014
Transcriptome Sequencing	Differential expression profiling	10-25M	Liu Y. et al., 2014; ENCODE 2011 RNA-Seq
	Alternative splicing	50-100M	Liu Y. et al., 2013; ENCODE 2011 RNA-Seq
	Allele specific expression	50-100M	Liu Y. et al., 2013; ENCODE 2011 RNA-Seq
	De novo assembly	>100M	Liu Y. et al., 2013; ENCODE 2011 RNA-Seq
DNA Target-Based Sequencing	ChIP-Seq	10-14M (sharp peaks); 20-40M (broad marks)	Rozowsky et al., 2009; ENCODE 2011 Genome; Landt et al., 2012
	Hi-C	100M	Belton, J.M et al., 2012
	4C (Circularized Chromosome Confirmation Capture)	1-5M	van de Weken, H.J.G. et al., 2012
	5C (Chromosome Carbon Capture Carbon Copy)	15-25M	Sanyal A. et al., 2012
	ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag Sequencing)	15-20M	Zhang, J. et al., 2012
	FAIRE-Seq	25-55M	ENCODE 2011 Genome; Landt et al., 2012
	DNAse 1-Seq	25-55M	Landt et al., 2012
DNA Methylation Sequencing	CAP-Seq	>20M	Long, H.K. et al., 2013
	MeDIP-Seq	60M	Taiwo, O. et al., 2012
	RRBS (Reduced Representation Bisulfite Sequencing)	10X	ENCODE 2011 Genome
	Bisulfite-Seq	5-15X; 30X	Ziller, M.J et al., 2015; Epigenomics Road Map
RNA-Target-Based Sequencing	CLIP-Seq	10-40M	Cho J. et al., 2012; Eom T. et al., 2013; Sugimoto Y. et al., 2012
	iCLIP	5-15M	Sugimoto Y. et al., 2012; Rogelj B. et al., 2012
	PAR-CLIP	5-15M	Rogelj B. et al., 2012
	RIP-Seq	5-20M	Lu Z. et al., 2014
Small RNA (microRNA) Sequencing	Differential Expression	~1-2M	Metpally RPR et al., 2013; Campbell et al., 2015
	Discovery	~5-8M	Metpally RPR et al., 2013; Campbell et al., 2015

ZARL1114

这个太有用了！一定要好好学习！