lc_extrap error: saturation

[aminakur]

When running lc_extrap, I receive the error
ERROR: Saturation expected at double initial sample size. Unable to extrapolate.

I read in the manual, that this problem can occur if the number of reads observed twice (n2) is greater than the number of reads observed once (n1). However, I quality checked my library and the percentages of duplicated reads are 6.5 and 6.7% (paired-end). Why did I get the message and what can I do?

[andrewdavidsmith]

There's nothing too unusual here. Yes, the manual says that this problem can occur in a particular situation (and typically that's what we see), but it's not the only reason. In general if we predict saturation so quickly, we are usually confident in that conclusion, but essentially nothing else. If you want more help with this, provide the counts histogram please.