SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Compare Genomes infrared1983 Bioinformatics 6 10-12-2011 01:29 PM
compare samples jgSoton Bioinformatics 2 10-03-2011 01:38 AM
Human DNA methylomes at base resolution show widespread epigenomic differences ECO Epigenetics 0 10-15-2009 08:29 AM

Reply
 
Thread Tools
Old 05-15-2013, 01:28 AM   #1
dnusol
Senior Member
 
Location: Spain

Join Date: Jul 2009
Posts: 133
Default how to compare methylomes

Hi, I am new to bisulfite sequencing and am confronted with an experiment where I would have to compare methylation states for several samples, some of which are paired (i.e. same individual, different tissues).
After some reading I have found Bismark to do methylation analysis on a one-by-one sample basis, if I am not wrong. I think I will be using Bismark for detecting methylation in a per sample basis.

But my question is, can anyone provide some guidelines as to how to compare samples after detecting methylation hotspots and if it is possible to take into account the pairing issue? Also, any references I can look for would be great.

Thanks

Dave
dnusol is offline   Reply With Quote
Old 05-22-2013, 01:04 AM   #2
dnusol
Senior Member
 
Location: Spain

Join Date: Jul 2009
Posts: 133
Default

In case it helps anyone, I found this article with one possible solution:

Bioinformatics. 2013 May 8.
Detection of Significantly Differentially Methylated Regions in Targeted Bisulfite Sequencing Data.
Hebestreit K, Dugas M, Klein HU.
dnusol is offline   Reply With Quote
Reply

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 07:33 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO