4.8 years ago by
How many tags do you have for treatment and how many do you have for control? Sounds like there is a just a big difference in the amount of data you have for each.
I think it's okay to use
mfold with a lower value, for instance 3,30. Although it depends. Let me explain. The
mfold parameter is used to build the shift model. The reason the shift model is important is it determines how much you have to shift your tags on the forward strand and the reverse strand. The theory is that when a transcription factor is bound at a particular spot, it causes a lag in opposite directions on both strands, because fragments tend to break at the point where the fragment is bound. Once
macs figures out how much to shift things it will shift tags forward on the forward strand and backward on the reverse strand.
To build this shift model, you want 'real' peaks. The mfold parameter is actually defining the definition of a peak. That way your model will be accurate. So,
-m 10,30 means that peaks that are about 10 fold to 30 fold enriched are going to be used as real peaks. The default values are just a guess (probably based on trial and error) and right values for your data could be different.
Anyway, in theory you could figure out what the shift in your data is yourself. There are ways to tackle this problem. (You can judge the level of fit of the current shift model by running the R script that macs produces.) Once you know the right shift size for your data, the whole issue of what mfold to use is irrelevant. You should just input your desired shift-size yourself and use the '
--nomodel' option. I don't think
macs does a great job of figuring out the shift-size anyway.
4.8 years ago by
KCC • 3.8k