I am doing an experiment on Cannabis sativa having a haploid genome size of 800 Mb. I have two groups (control and treatment) with 3 replicates each.

How many reads should I go for?

Does the sex of the plant matter as it is a monoecious plant?

I need to take the sample at 3 - 4 leaf stage and I won't know the sex of the plant at that time.

What should I do? Increase biological replicates? or its fine coz I'm studying stress response?

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