How to find the epigenetic pattern of a LIST of a specific genomic location ?

Question

[Zakaria Benmounah]

Hi,

I'm wondering how to find the epigenetic pattern of a LIST of a specific genomic location ?

Thanks

[karl.stamm]

What do you want to do with the list of locations? Most tools accept BED format, so first reformat your data into a BED file. Then we have to figure out what you mean by an epigenetic pattern.

[Zakaria Benmounah]

My file in that format:

chr1: 11876
chr1:33564
chr4: 57575

with more than 15 thousand lines so I need to know for example the DNA methylation status at each of these locations,

[karl.stamm]

Methylation is an active process, with cells activating it and deactivating it dynamically. You'll need to specify a time point, or cell type, then find an experiment where someone did a capture and published the results. They probably publish Chip-seq peaks as BED files, so you can search that BED with your BED by using BEDTOOLS intersectbed. Problem is it will be specific to the cell line they studied. Epigenetics isn't like a published genome reference.

The ENCODE project might be a good place to start.

[Zakaria Benmounah]

Karl many many thanks that what I was looking for "BEDTOOLS intersectbed",

and yes I have a specific tissue to look for.

Best

Zack

Answer 1

[Floris Brenk]

http://epigenomegateway.wustl.edu/

http://www.epigenomebrowser.org/

http://genomebrowser.wustl.edu/

[Zakaria Benmounah]

Thanks Floris, but I have a list of more than 15 thousands positions, I can't look at each alone, I need software or browser where we can upload file by indicating the name of the chromosomes and the positions for example:

chr1: 11876
chr1:33564
chr4: 57575

and so on,

many thanks