I have been trying to find tools to estimate fragment length for single end ChIP-seq data. I've been able to get some success with Homer's makeTagDirectory and MaSC but I wanted to triple check my numbers with another tool. Q is able to estimate the average fragment length as well as part of its peak calling. I was wondering if anyone has used it as it is relatively new and what they think of it? Can it be run on a mac system?
Or if you have any other recommendations of tools to estimate fragment length for single-end read data?