I am struggling to find references that would guide my experimental design. Specifically, I am trying to determine optimal sample size for a differential ChIP-seq experiment involving farm animals. I would like to investigate differential TF binding in affected vs. unaffected animals. Compounding variables may include age and/or farm differences. Breed will be the same.
The ENCODE consortium recommends a minimum of 2 replicates, but that seems to refer to a simple ChiP-seq experiment defining binding sites, rather than differential binding between two groups.
I have found the following articles, but find they don't address the issue directly:
- Zuo C, Keleş S. A statistical framework for power calculations in ChIP-seq experiments. Bioinformatics. 2014;30(6):753-760. doi:10.1093/bioinformatics/btt200
Zhao, S., Li, CI., Guo, Y. et al. RnaSeqSampleSize: real data based sample size estimation for RNA sequencing. BMC Bioinformatics 19, 191 (2018). https://doi.org/10.1186/s12859-018-2191-5
Chung-I Li, David C Samuels, Ying-Yong Zhao, Yu Shyr, Yan Guo, Power and sample size calculations for high-throughput sequencing-based experiments, Briefings in Bioinformatics, Volume 19, Issue 6, November 2018, Pages 1247–1255, https://doi.org/10.1093/bib/bbx061
Any help is greatly appreciated.