Hello all!
I want to perform WGBS with sheep DNA samples. Due to funding restrictions I have to choose between sequencing deep or biological replications. What would it better, to sequence 3 control and 3 affected sheep ( ≈ 40x) or 6 controls and 6 affected ( ≈ 8x)?
Thanks!
DNA Methylation Data Analysis Workshop
How to use bisulfite-treated sequencing to study DNA methylation
When?
12-15 November 2019
Where?
Berlin, Germany
Link?
https://www.ecseq.com/workshops/workshop_2019-07-NGS-DNA-Methylation-Data-Analysis
Ziller et al. 2014 addressed this question in a really nice paper ( https://www.nature.com/articles/nmeth.3152 ). If you take a look at Fig. 2A in this paper, you can achieve a true positive rate (TPR) of 80 at a coverage of ~5x with 3 biological replicates. This was not achievable with two replicates at a coverage of 30x. They also find that they observed diminishing returns when increasing coverage past 10x for a single replicate, whereas increased sensitivity when they increased the number of biological replicates at the same coverage.
The moral of this paper? It may be that increased biological replicates will achieve a higher TPR than deeper sequencing. Based on this, I would say increased biological replication may be better off.
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