Hi all,

I have some collaborators using INDUCE-seq to map the position of double-strand breaks (https://www.biorxiv.org/content/10.1101/2020.08.25.266239v1). The output is a series of bed files giving the location of double-strand breaks - essentially a huge bed file of single-nucleotide positions.

A question we have is whether any particular cytobands are over-represented for double-strand breaks. Is there any package or function in BioC that can do this? It would be a similar question to whether SNPs are over-represented in any particular cytoband - if anyone has done this. I guess I need to make a chi-squared test for each cytoband using the number of bases in the band that have double-strand breaks compared to the number of breaks in the genome overall. There's probably a smarter way though.

Thanks,

Mark