I am working on an experiment in which we are going to be doing reduced representation bisulfite sequencing and RNA-seq. Our plan is to pool the samples for each treatment group and sequence each treatment group as a single sample. So for example if we have 4 samples for treatment A we will combine them and sequence the group as a single treatment A sample.
My question is when using this method are there any issues with comparing pools of different sample size? I have two treatments, one has 4 samples and the other has 5. Can I use all the samples from each treatment, or do I have to remove one from the second group, so I have pools of 4 samples for each group?
In other words, is there any issues associated with comparing pools with unequal sample size?
My question is when using this method are there any issues with comparing pools of different sample size? I have two treatments, one has 4 samples and the other has 5. Can I use all the samples from each treatment, or do I have to remove one from the second group, so I have pools of 4 samples for each group?
In other words, is there any issues associated with comparing pools with unequal sample size?
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