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Oct 26, 2020

ChIP-seq sequencing depth guidline

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
. 2013 Nov; 9(11): e1003326. 
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003326 


Impact of sequencing depth in ChIP-seq experiments
. 2014 May 1; 42(9): e74.
https://academic.oup.com/nar/article/42/9/e74/1248114


What is the minimum million reads that I need to have a good result of chip-seq in human?
https://www.researchgate.net/post/What_is_the_minimum_million_reads_that_I_need_to_have_a_good_result_of_chip-seq_in_human


Recommended Coverage and Read Depth for NGS Applications
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 ~5-8MMetpally RPR et al., 2013; Campbell et al., 2015

References:

  • Ajay, S.S et al. Accurate and comprehensive sequencing of personal genomes. Genome Research 21, 1498 (2011).
  • Belton, J.M. et al., Hi-C: a comprehensive technique to capture the conformation of genomes. Methods, 58, 221-230 (2012).
  • Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53–59 (2008).
  • Campbell J.D. et al., Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data. RNA 21, 164-171 (2015).
  • Cho J. et al., LIN28A Is a Suppressor of ER-Associated Translation in Embryonic Stem Cells. Cell 151, 765-777 (2012).
  • Clark, M. J. et al. Performance comparison of exome DNA sequencing technologies. Nature Biotech. 29, 908–914 (2011).
  • ENCODE 2011 Genome Guidelines
  • ENCODE 2011 RNA-Seq Guidelines
  • Eom T. et al., NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure. Elife 2, e00178 (2013).
  • Epigenomics Road Map Guidelines
  • Feng, H. et al. Reducing INDEL calling errors in whole genome and exome sequencing data. Genome Medicine 6, 89 (2014).
  • Landt, S.G. et al., ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research, 22, 1813-1831 (2012).
  • Liu Y., et al., RNA-seq differential expression studies: more sequence or more replication? Bioinformatics 30(3):301-304 (2014).
  • Liu Y., et al., Evaluating the impact of sequencing depth on transcriptome profiling in human adipose. Plos One 8(6):e66883 (2013).
  • Long, H.K. et al., Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. eLIFE 2, e00348 (2013).
  • Lu Z. et al., RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins. Genome Biology 15:R7 (2014).
  • Maynert et al., Quantifying single nucleotide variant detection sensitivity in exome sequencing. BMC Bioinformatics 14, 195 (2013).
  • Medvedev, P. Detecting copy number variation with mated short reads. Genome Research 20, 1613 (2010).
  • Metpally RPR et al., Comparison of Analysis Tools for miRNA High Throughput Sequencing Using Nerve Crush as a Model. Frontiers in Genetics 4:20 (2013).
  • Rogelj et al., Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain. Scientifc Reports 2, 603 (2012).
  • Rozowsky, J.et al., PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nature Biotech. 27, 65-75 (2009).
  • Sanyal, A. et al., The long-range interaction landscape of gene promoters. Nature, 489, 109-113 (2012).
  • Sugimoto Y et al., Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biology 13:R67 (2012).
  • Taiwo, O. et al., Methylome analysis using MeDIP-seq with low DNA concentrations. Nature Protocols 7 617-636 (2012).
  • van de Weken, H.J.G. et al., Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nature Methods 9, 969-972 (2012).
  • Xie, C. & Tammi, M. T. CNV–seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10, 80 (2009).
  • Zhang, J. et al., ChIA-PET analysis of transcriptional chromatin interactions. Methods 58 289-299 (2012).
  • Ziller, M.J et al., Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing. Nature Methods 12, 230-232 (2015).

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