The tools to plot the saturation curve for RNA-Seq

Question

[wangdp123]

Hi there,

Does anybody know a decent tool that can plot the saturation curve for RNA-Seq data in order to estimate how many reads will be enough to accurately measure the stable gene expression levels?

I tried to search but couldn't get a clear answer.

Thank you very much,

Tom

Answer 1

[Martombo]

On RSeQC there is a tool to measure splice junction saturation. It's hard to know how much coverage you would need to measure all genes, since there can be many that are lowly expressed or present in a small subset of a heterogeneous sample and it's difficult to draw a hard line.