搜索
查看: 2603|回复: 1

不同组学研究建议采用的测序策略

[复制链接]

58

主题

103

帖子

756

积分

版主

Rank: 7Rank: 7Rank: 7

积分
756
QQ
发表于 2017-4-23 17:25:07 | 显示全部楼层 |阅读模式
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
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
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
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
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
>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
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
~1-2M
Metpally RPR et al., 2013; Campbell et al., 2015
Discovery
~5-8M
Metpally RPR et al., 2013; Campbell et al., 2015




上一篇:给aws扩容-亚马逊云
下一篇:赛福基因公开课第一节《基因检测简介》
回复

使用道具 举报

13

主题

31

帖子

263

积分

中级会员

Rank: 3Rank: 3

积分
263
发表于 2017-4-27 23:23:55 | 显示全部楼层
这个太有用了!一定要好好学习!
回复 支持 反对

使用道具 举报

您需要登录后才可以回帖 登录 | 立即注册

本版积分规则

QQ|手机版|小黑屋|生信技能树 ( 粤ICP备15016384号  

GMT+8, 2019-10-21 09:20 , Processed in 0.043883 second(s), 26 queries .

Powered by Discuz! X3.2

© 2001-2013 Comsenz Inc.