rlsim: relationship between expression, number of fragments and coverage depth

Question

[ernesto.picardi]

Hi all,

I have a couple of questions regarding the relationship between transcript expression, number of fragments and coverage depth. I know that we cannot define a real coverage depth in trascriptome studies. However, in a simulated experiments I may require a predefined coverage depth given the number of fragments and transcript expression. So, how can I have an idea of expected coverage depth per a given transcript given its length, expression and number of fragments? Many thanks in advance. My idea is to simulate a transcriptome in which I know the expected coverage depth (even though this coverage is not uniform along the transcript).

Best,

Ernesto

[biotech]

expected coverage = expression - length - number of fragments