Go Back   SEQanswers > Applications Forums > Epigenetics

Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-PET and paired-end RNA-Seq rulerwoods RNA Sequencing 3 04-10-2012 08:18 AM
Any experience with BGI? iquigley Core Facilities 9 11-15-2011 11:39 PM
PET-seq analysis bogdan Bioinformatics 0 08-25-2009 10:36 PM
ChIP - PET data analysis bogdan Bioinformatics 0 05-18-2009 05:42 PM
NGS of paired-end tags (PET) for transcriptome and genome analyses Melissa Literature Watch 0 04-24-2009 06:46 AM

Thread Tools
Old 05-09-2011, 12:46 PM   #1
Location: Stockholm, Sweden

Join Date: Oct 2009
Posts: 62
Default Experience with ChIA-PET?

Hi All,

We are looking into ChIA-PET, a tool to look at genome wide chromatin interaction analysis. So far all publications seems to be from the group developing the procedure (PMID: 20181287 & 19890323). Does anyone out there have any experience with this technique, and any comments regarding the sensitivity and specificity, the pros and cons? Would be highly appreciated.

Boel is offline   Reply With Quote
Old 06-22-2011, 03:04 AM   #2
Junior Member
Location: Cambridge, UK

Join Date: Mar 2009
Posts: 6

So are we. Should one interpret the lack of replies as CHIA-PET being really challenging?
arendon is offline   Reply With Quote
Old 06-23-2011, 12:19 AM   #3
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

We've done a fair bit of work with this kind of data, and I'm currently writing tools for handling this kind of paired sequence data which will appear in a future version of SeqMonk.

It's difficult to make general observations about this type of data as many of the problems we see are technical in nature and relate to the specific types of protocol being used (of which there are several related variants). I think it's fair to say that extracting biologically relevant information from these data is still very challenging, and it's pretty easy to draw incorrect conclusions by not accounting for factors which might introduce systematic bias in the frequency of interaction pairs you see. Also, if you're doing a comprehensive unbiased analysis then the volume of data is really problematic. Exponential increases in interactions from linear increases in measurement sites is no fun (well actually it is kind of fun in a masochistic way)!
simonandrews is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:14 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO