Question: Software To Analyse Chromatin-Interaction Sequencing Datasets?
7
gravatar for Ahdf-Lell-Kocks
8.2 years ago by
Ahdf-Lell-Kocks1.6k
Ahdf-Lell-Kocks1.6k wrote:

I am interested in knowing what software is out there to analyse chromatin-interaction sequencing datasets like those coming from genome-wide next-gen sequencing ChIA-PET protocols:

http://noble.gs.washington.edu/proj/yeast-architecture/

So far I've only seen generic clustering tools being re-purposed for chromatin interaction analysis but nothing more.

software interaction • 2.8k views
ADD COMMENTlink modified 8.1 years ago by Gjain5.4k • written 8.2 years ago by Ahdf-Lell-Kocks1.6k
4

I still can't take the ChIA-PET method seriously... http://en.wikipedia.org/wiki/Chia_Pet

ADD REPLYlink written 8.1 years ago by Casey Bergman18k
1

@Casey: I completely agree with you.

ADD REPLYlink written 8.1 years ago by Gjain5.4k

What kind of analysis?

ADD REPLYlink written 8.2 years ago by Gjain5.4k

I added a link to an example paper where they produced the datasets: http://noble.gs.washington.edu/proj/yeast-architecture/

ADD REPLYlink modified 4 months ago by RamRS25k • written 8.1 years ago by Ahdf-Lell-Kocks1.6k

Indeed, this has been a problem for the advancement of this technique :-)

ADD REPLYlink written 8.1 years ago by Ahdf-Lell-Kocks1.6k
3
gravatar for Neilfws
8.1 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

Quick web search threw up ChIA-PET tool. Described as "a software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser."

ADD COMMENTlink written 8.1 years ago by Neilfws48k

This is developed by the group that originally developed ChIA-PET, so it's a good start.

ADD REPLYlink written 8.1 years ago by Mikael Huss4.7k

I wonder if you tried this software package. The document is very short and lack of necessary information. I have not found a way to use it. Could you give some suggestions?

ADD REPLYlink written 8.0 years ago by Ct586540

As I say, quick web search - have not tried it myself.

ADD REPLYlink written 8.0 years ago by Neilfws48k

I was wondering if anyone has tried this tool since this was posted. We are trying to install this tool and get only problems with the pipeline. The manuals are VERY unhelpful and the authors of the papers are not so supportive. So I would like to know if anyone has any success in running the pipeline

ADD REPLYlink written 6.9 years ago by Assa Yeroslaviz1.3k
3
gravatar for Gjain
8.1 years ago by
Gjain5.4k
Munich, Germany
Gjain5.4k wrote:

MizBee: A Multiscale Synteny Browser alt text

ADD COMMENTlink written 8.1 years ago by Gjain5.4k
2
gravatar for Casey Bergman
8.1 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

Hi-C/5C interaction data can be analyzed using methods from the Dostie Lab:

ADD COMMENTlink modified 5 months ago by RamRS25k • written 8.1 years ago by Casey Bergman18k

you can also use the my5C tool to analyze the 3C, 5C and hi-C datasets on http://3dg.umassmed.edu/welcome/welcome.php

ADD REPLYlink written 8.1 years ago by Gjain5.4k

@Gjain - I thought about posting my5C, but it doesn't appear to allow you to analyze your own data.

ADD REPLYlink written 8.1 years ago by Casey Bergman18k

@Casey : yes,its ambiguous right now just to data analysis. We have developed a new pipeline and updated the web tool. We are going to replace the current one with refined data analysis and supporting tools soon.

ADD REPLYlink written 8.1 years ago by Gjain5.4k
1
gravatar for Larry_Parnell
8.2 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

You might want to look at the approach applied by Jonathan Pritchard and colleagues in associating DNA methylation patterns with variation in genetic markers and in gene expression. Their paper (Bell, et al) and data can be found here.

ADD COMMENTlink written 8.2 years ago by Larry_Parnell16k
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