Tool: Chance: Comprehensive Software For Quality Control And Validation Of Chip-Seq Data
gravatar for Aaron Diaz
5.4 years ago by
Aaron Diaz20
San Francisco, CA
Aaron Diaz20 wrote:

Hi, We at UCSF have recently developed a software tool for ChIP-seq quality control and protocol optimization called CHANCE, which appears in the current special issue of Genome Biology:

CHANCE has a graphical interface and doesn't require any knowledge of programming or statistics. The CHANCE program as well as the source code can be downloaded from:

thanks, Aaron Diaz Inst. for Human Genetics, UCSF

chip-seq quality next-gen qc tool • 2.7k views
ADD COMMENTlink modified 19 months ago by paul.e.gradie60 • written 5.4 years ago by Aaron Diaz20
gravatar for paul.e.gradie
19 months ago by
Australia/Melbourne/University of Melbourne
paul.e.gradie60 wrote:

Wow - no updates to this?

Who is going to use this if it can't accommodate mm10?

I'll put an alternative out there: DeepTools.

These guys did a fantastic job of coding up a suite of tools for assessing sequencing results. Most importantly for ChIP, it provides the Plot_Fingerprint tool for using SES (signal extraction scaling) to asses enrichment strength. The original paper that both CHANCE and DeepTools based this on can be found here:

Its clean, beautiful, and the source code is written in Python (so if you're like me and looking for a large Python project to digest, this is your ticket!)

Cheers, Paul

ADD COMMENTlink written 19 months ago by paul.e.gradie60
gravatar for André Rendeiro
4.1 years ago by
Vienna, Austria
André Rendeiro50 wrote:

I heard about CHANCE recently and just for curiosity would like to run it on my data which is from unsuported organisms.

I can't find any manual reference on how to add a custom build to use in CHANCE.

Adding annotation for a custom genome shouldn't be too difficult, unless the currently supported builds (hg18, hg19, mm9) are for some reason hard-coded in the CHANCE code. Before I start looking more deeply into this, has anyone tried to do this?

ADD COMMENTlink written 4.1 years ago by André Rendeiro50

Hi André, did you manage to run it on a custom build? 

ADD REPLYlink written 2.7 years ago by sinha0
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