Question: Does H3K27ac generate narrow or broad peaks?
0
gravatar for jklopp
2.1 years ago by
jklopp0
jklopp0 wrote:

Hi,

I have been trying to find out whether the H3K27ac Histone modification generates sharp or broad peaks during a ChiP-Seq experiment and therefore to either use the "--broad"-flag in macs2 or not.

Several studies I found (http://www.nature.com/nrg/journal/v12/n1/full/nrg2905.html for example) mentioned that H3K27me3 "and other" histone modifications generate broad peaks but H3K27ac was never explicitly addressed.

In contrast some studies (https://www.researchgate.net/publication/299653522_Identification_of_Epigenetic_Biomarkers_of_Lung_Adenocarcinoma_through_Multi-Omics_Data_Analysis) even treat H3K27ac as narrow peak creating but unfortunately lack suitable sources.

I really appreciate your help!

broad peak macs2 h3k27ac chip-seq • 2.1k views
ADD COMMENTlink modified 2.1 years ago by Devon Ryan90k • written 2.1 years ago by jklopp0
4
gravatar for Devon Ryan
2.1 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

H3K27ac is a sharpish mark, so you can start with the defaults.

@kennethcondon2007: Some marks (e.g., H3K4Me3) are known to produces sharp distinct peaks. Other marks (e.g., H3K9me3) produce wide >10kb regions of enrichment. ChIPseq itself isn't any noisier than ATACseq or anything else, the noise is due to the underlying biology.

ADD COMMENTlink written 2.1 years ago by Devon Ryan90k

Clarification always help, thank you :)

ADD REPLYlink written 2.1 years ago by YaGalbi1.4k
0
gravatar for YaGalbi
2.1 years ago by
YaGalbi1.4k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.4k wrote:

All the broad flag does is combine narrow peaks that are very close together into 1 peak. Run MACS2 with 1) broad, 2) narrow and 3) gapped options and then view the 3 results in IGV and you'll see it clearly.

Not so sure about the next bit but my 2 cents is...:

I dont think the mark itself produces the "broad" they are referring to. I think the use of the word "broad" is referring to resolution or noise of Chip-seq data, for example ATAC-seq data would be expected to produce narrower peaks than Chip-seq data.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by YaGalbi1.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 978 users visited in the last hour