Tutorial: Video: Visualization of whole genome DNA methylation data in IGB
11
gravatar for Nowlan Freese
4.3 years ago by
Nowlan Freese850
United States
Nowlan Freese850 wrote:

“Focus on a Feature: Visualization of whole genome DNA methylation data in IGB.”

This tutorial has ended. You can find the recording here:

 

To follow along, you can find the data I used in Galaxy here.

You can find previous Focus on a Feature tutorials here.

Program:

  1. Intro to generating whole genome bisulfite sequencing (BS-seq) data.
  2. Differential visual analysis of BS-seq data in IGB.
  3. Comparative visualization with RNA-Seq data.

Integrated Genome Browser (IGB)

IGB provides an advanced, highly customizable environment for exploring and analyzing large-scale genomic data sets. Using IGB you can visually analyze RNA-Seq, ChIP-Seq, and many other genomic projects. The best part is that IGB can be used to produce publication quality images from genome scale data sets, and is provided FREE.

 

If you have questions or need assistance, contact us at: 

Nowlan Freese nfreese@uncc.edu

Ann Loraine aloraine@uncc.edu

 

To download and start IGB, go to bioviz.org and select the "Download Now" link.

Once IGB starts, choose Help / Tutorials for a quick introduction to IGB.

 

**Please share this with students and colleagues**

rna-seq bismark igb tutorial bs-seq • 3.2k views
ADD COMMENTlink modified 3.6 years ago by Antonio R. Franco4.1k • written 4.3 years ago by Nowlan Freese850
1

I've been following a repeating the tutorial. Very nice indeed..

I have a question for you. How do you manage the data ? Is it required any type of normalization ?

ADD REPLYlink written 3.6 years ago by Antonio R. Franco4.1k

Hi Dr. Franco,

The methods that have been recommended to me for analyzing methylation data can be found in two papers: "Human body epigenome maps reveal noncanonical DNA methylation variation" and "Charting a dynamic DNA methylation landscape of the human genome". The supplementary information goes into detail on calling the methylation rates using a binomial test, as well as determining differentially methylated regions between samples. 

Nowlan

ADD REPLYlink written 3.6 years ago by Nowlan Freese850
1
gravatar for Antonio R. Franco
3.6 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.1k wrote:

I wrote a letter of support last year, and I have just wrote another one, because this program is fantastic.

Please, visit the web page and include a supporting letter

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Antonio R. Franco4.1k
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