Has anyone had experience with Q for ChIP-seq peak calling?

Question

[Sadia]

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?

[Devon Ryan]

You don't have the output from a bioanalyzer run? I would think that'd be more reliable.

[Ming Tommy Tang]

see https://github.com/crazyhottommy/ChIP-seq-analysis/blob/master/part0_quality_control.md#encode-guidlines

Answer 1

[igor]

MACS does fragment length estimation, which I found to be fairly accurate. It's a popular tool, so it should be relatively easy to install and run.

[Devon Ryan]

Good catch, it's the predictd program from MACS.

Answer 2

[Sinji]

SPP from phantompeakqualtools does fragment estimation and I believe it's what the ENCODE pipeline uses.