Now, I have a set of TF binding site files with two replicates. After some basic statisitics, I found that many TF peak regions location are not identical but overlapped between these two files.
So, does anyone has some good ideas to deal with TF binding site data like this?
For example,
Peak region 1 in FILE ONE: chr1 1000 1200
Peak region 1 in FILE TWO: chr1 1120 1250
These two peaks are overlapped with each other, but I want to know how to set a threshold objectively to determine whether two overlapped peaks could be merged as one.
So, does anyone has some good ideas to deal with TF binding site data like this?
For example,
Peak region 1 in FILE ONE: chr1 1000 1200
Peak region 1 in FILE TWO: chr1 1120 1250
These two peaks are overlapped with each other, but I want to know how to set a threshold objectively to determine whether two overlapped peaks could be merged as one.
