I have obtained binding locations of a specific protein on DNA by CHIP-seq. My hypothesis is that within those regions in specific cancer type, I expect to see higher mutation rate than random regions. I think, bootstrapping could solve the solution by comparing random vs my bed file.
For this reason, I searched through biostars and I found that bedtools shuffle is a viable option.
I generated these randomly shuffled bed files with this specific command.
shuffle -chrom -i highconf_250wider.bed -g /Users/morova/bedtools/GRCh37.genome.txt
Is there a way to validate that shuffling executed as I expected. For example there is also ChromFirst option. Is there a statistical method that you guys should suggest me ?
Thank you very much,