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


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


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.


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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