Pooled samples for methyl seq of population data

[NABOT]

Hi
I am interested to find the differential methylation pattern in two population of same plant species.
Will it be appropriate to pool, say 25 plants from each population and consider it as one sample

[dpryan]

No, it would not.

[NABOT]

Thanks dpryan, what would be ur suggestions ? multiple individual from each populations?

[dpryan]

Yeah, you'll be better off sequencing a number of individual samples at lower depth. By pooling and only then sequencing one pool per group, you're unable to estimate biological variability. Consequently, you wouldn't be able to look for statistical differences (some people have incorrectly used fisher's exact test in this situation, don't do that, it's wrong).