Question: Does MACS score correlate with binding strength
1
gravatar for varsha619
2.5 years ago by
varsha61990
varsha61990 wrote:

Hello, I know the MACS score is -log10 of p-value, used to get the significant ChIP-seq binding peaks over the control. Does MACS score from MACS14 also correlate with ChIP binding strength? i.e, does higher the score equal more binding at that region or higher affinity of binding? I appreciate your help, just trying to understand the biological meaning of the score better.

chip-seq macs • 989 views
ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 2.5 years ago by varsha61990
2

affinity is a different thing that abundance. if you look at the wiggle/bigbed files for your ChiSeq you can check "how much" binding you have. however, none of this will tell you the "strength" of binding. you need wet lab experiments mutating the binding site to determine that.

ADD REPLYlink written 2.5 years ago by TriS4.2k

That makes sense, thank you so much!

ADD REPLYlink written 2.5 years ago by varsha61990
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