PLoS Comput Biol. 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
Nucleic Acids Res. 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 | ~5-8M | Metpally 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).
