I have a list of interesting genomc regions (intergenic regions, a few 100 bases long) and I want to compare enrichment of various histone modifications between these regions, using previously published ChIP data. One way of doing this is to download specific data sets from modENCODE, convert them to bed files then use simple grep-type commands (probably in python) to retrieve the enrichment value for each locus. While this works in principle, it's somewhat slow. I know that there is a tool called modMINE that lets you get this sort of information through database queries, but I didn't have any luck when searching for specific histone modifications.
Is there a better way of doing this?
Is there a better way of doing this?
