I have been trying to call peaks for a transcription factor using the last release of macs2.1, I have used it effectively with default parameters for chromatin marks but while am trying to use it for TFs , it gives excessively low peaks with default. So as per the warning am intending to change the mfold parameter but am unable to since it throws an error. How to change the mfold parameter in macs2.1, what is the syntax for it. I want to use an mfold which is as low as 5,30 the default is 5,50. With macs1.4 I was getting 450 peaks but with macs2.1 am getting 60 peaks.
Warning
"Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model!"
So I am trying to run lowering the mfold. I am keeping the shfit size and bandwidth same. Did anyone face this problem? I am unable to change the mfold. It throws an error.
Thanks
VD
