Get average interaction submatrices from pre established contact file

[Lucas446]

Hi,

I would like to perform an PE-SCAn but not all-vs-all contact but rather from a bed file containing contacts (bedpe) (chr1 start1 end1 chr2 start2 end2), and I would like PE-SCAn to only look at those contacts, is it possible or is it through another GENOVA tools ?

Thanks a lot,
Best,
Tanguy

[teunbrand]

Hi there, this sounds a lot like the APA() function. Does this fit your needs?