Meaning of mfold upper limit?

Hi, all!

I've been working on ChIP-seq data using 'MACS2', and am confused by "mfold".

Does "mfold" represent the relative enrichment against control (IgG or genomic fragments) or background noises in the test sample?

And why there's a upper limit in "mfold"? Does that mean fold-enrichment over a certain level is not considered as a peak? Why?

Please, someone explain them to me!

Thank you

mfold macs2 chip-seq

• 1,537 views • link

written 8.0 years ago by mbk0asis

0 answers

No answers yet.

More posts like this

What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
written 2.3 years ago by HyperEvo •

Hello everyone. I am analyzing an ChIP-seq peak set and I wonder what is the real meaning of the relative enrichment or height of called …
Understanding Homer output for makeTagDirectory
written 2.5 years ago by Assa Yeroslaviz

I was wondering where I can find explanation about the output given to me by homer's `makeTagDirectory` command. one of the files return this output: …
Does it make sense to consider a genomic loci when there is no peak but high signal?
written 7.8 years ago by venu

Hi all, The question is related to ChIP-seq, whether we should (at least in my case), consider a genomic loci with high IP signal over …
Input control for ChIP-seq. [Seeking for the clarification between "Library DNA conc.", "no. of raw…
written 8.6 years ago by chiefcat

Hi all, Although the Input control is commonly used for in ChIP-seq. analysis (e.g. for normalization, as background for peak calling), it seems hard to …
MACS for chip-seq: difference between sonication size(bandwidth) and fragment size?
written 8.7 years ago by salamandra

In MACS algorithm article (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r137) for chip-seq says: "Given a sonication size (bandwidth) and a high-confidence fold-enrichment (mfold), MACS slides 2bandwidth windows across the genome …
cross strand correlation in BrU-UV ChIP data
written 9.3 years ago by mforde84

Hi, We did a anti-BrU pulldown for two biological replicates, merged tag densities, and called peaks with input control from an IgG pulldown. I generated …
how to find differential region between my replicates.
written 9.5 years ago by maryamforoozani16 •

Hello , I did chip experiment with three replicates for two conditions ( normal condition(C) and phosphate deficiency condition (P)) on Rice genome. I tried …
MACS Lambda Local
written 9.6 years ago by Rishikesh Lotke •

Hello everyone, Could someone please provide a working example (or point me to a good resource) of how 'lambda local' (along with lambda BG, 1k …
Extension size problem in MACS2
written 9.7 years ago by anu014

Greetings of the day Biostars! Recently, I have run a lot of chip-seq samples. All were having their respective controls. According to MACS2 user manual, …
Issues related to HOMER
written 11.7 years ago by pinky_pinkpinky •

Hi all, Can any one help me in resolving this issues. While creating the Tag directory I got this problem. ``` !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Average reads per …