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6

We sequence and therefore typically report assemblies as DNA sequences, even if they're actually RNA.


-1

How can anyone answer this without knowing exactly what you are looking at? But RNAs are very commonly represented as their DNA equivalent


1

Not all cells will perform the same sequence of transcriptional changes. The paragraph you quote simply states that differentiation isn't a step change with all cells differentiating at the exact same moment. Rather, it's a more gradual change with cells each working on their own time scale.


2

Based on back and forth in the comments, I think that you might be interested in a deep mutational scanning workflow, for example dms_tools2 or enrich2. These are built specifically for the kind of experiment that you are interested in, if I understand correctly. See attached figure from dms_tools2:


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