Using Bayespeak for Paired-end reads

Question

[Nathan]

Hi everyone,

I was wondering if anyone knew how well BayesPeak performs on paired-end ChIP-seq reads (MNase-treated) - or even if it can be ran on paired-end reads reliably?

I noticed in the original BayesPeak paper that its says that the model can be easily extended to accomodate paired-end reads, but I have not being able to find any documentation about using BayesPeak on paired-end data.

Has anyone used BayesPeak to do this.....is the best way just to treat the paired-end reads as single-end reads or leave them fully mapped as one contiguous fragment in this analysis?

I have tried to contact the author/maintainer of the package but it looks like his email address has been discontinued.

Thanks in advance.