Hi,

I am not sure if this is the expected function behavior or if it is a possible bug.

I have very deep RNA seq data. I am trying to plot the pileup, I observe peaks at the start of some exons, Those peaks do not appear in IGV.

But when I change the max_depth option to my max depth the peaks disappear, and the read depth is precisely the same as in IGV. Is that a bug? If not, could you explain to me, what is happening?

From the documentation, max_depth only count max_depth overlapping reads.

But if so :

1- why are those peaks?

2- in my case, why is not everything max out?

I may have a confusion about what is called overlapping reads...

The only thing I changed between those two plots is the max_depth option.

I greatly appreciate your help,