SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Why is it necessary to visualize the RNA-seq data in a genome browser? pinki999 Bioinformatics 4 08-05-2013 08:13 AM
is is possible to visualize RNA-seq data in UCSC genome browser(ENCODE)? HSV-1 RNA Sequencing 5 07-21-2012 06:24 PM
Genome Browser to visualize RNA-Seq Data Dolphin22 Bioinformatics 4 07-04-2012 07:38 AM
Identify and visualize differentially expressed genes from RNA-Seq data? mediator Bioinformatics 7 05-09-2012 12:00 AM
Visualize pair-end RNA-Seq in UCSC browser oscarluoinau Bioinformatics 0 11-21-2011 01:24 AM

Reply
 
Thread Tools
Old 09-24-2013, 08:42 PM   #1
icyeyes1
Junior Member
 
Location: Seoul, Korea

Join Date: Sep 2013
Posts: 1
Default How visualize the BS-seq profiles?

Hi, I'm newbee for NGS, especially BS-seq,
though my PI think I should be able to manipulate the data.

I have good qual BS-seq data, and I could map the the data with
BS-seq-specialized tools, such as BISMARK etc.

Though I could not visualize any general data what found from several papers.
(Specially for methylation profiles around genes or TE; DMR peak calculation (not DMC))

Do you have any recommendations ?
I am slightly available for R; though no sufficient tools was found.

hope for your good days.
icyeyes1 is offline   Reply With Quote
Old 09-25-2013, 12:20 AM   #2
simonandrews
Simon Andrews
 
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871
Default

You can certainly construct these kinds of plot in SeqMonk. There's a tutorial video here which goes through the process of constructing a methylation trend plot.

I'm not aware of a tool which directly supports this sort of plot in R, but you could make something out of the core R components relatively easily by just tiling graphs togehter.
simonandrews 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 05:59 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO