Hi all,

I'm wondering if it is possible to compare MN-ase and FAIRE (or DN-ase) results.

I tried to compare it using bedtools intersect -v to count features shared and not-shared between files. In theory, MN-ase gives opposite results to FAIRE or DN-ase. So great number of not shared features would mean that methods gives consistent results.

BUT, the coverage of MN-ase data is very low (0.53%) so it is very easy to hit with FAIRE peak in the interval not present in MN-ase data - so it inflate positive result.

Some features are covered by intervals from both files (ie. negative MN-ase and positive FAIRE), for such features I have run a t-test comparing length of overlap of intervals in each file. Still it doesn't seem valid.

Is there any way to compare such datasets?