Question: Has anyone had experience with Q for ChIP-seq peak calling?
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gravatar for Sadia
3.6 years ago by
Sadia50
Sadia50 wrote:

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?

chip-seq • 1.3k views
ADD COMMENTlink modified 3.6 years ago by Sinji3.0k • written 3.6 years ago by Sadia50

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

ADD REPLYlink written 3.6 years ago by Devon Ryan95k
3
gravatar for igor
3.6 years ago by
igor11k
United States
igor11k wrote:

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.

ADD COMMENTlink written 3.6 years ago by igor11k

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

ADD REPLYlink written 3.6 years ago by Devon Ryan95k
0
gravatar for Sinji
3.6 years ago by
Sinji3.0k
UT Southwestern Medical Center
Sinji3.0k wrote:

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

ADD COMMENTlink written 3.6 years ago by Sinji3.0k
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