Hi everyone, 
I would like to ask how, or whether, proportional read counts (read proportions) can be used appropriately. Are these data already normalized ? (I am unsure whether I should still select the normalization option on the input page).
They are neither classical abundances nor raw read counts. What would be the correct way to handle this type of data?
In addition, I have two merged sequencing runs, so I assume that CLR transformation may be necessary because of the compositional nature of the data and potential run/batch effects. Can CLR transformation be applied to proportional read counts, or is some additional preprocessing required beforehand (e.g., adding a pseudo-count because of zeros)?
Thank you 