Does there exist a BED file of CTCF ChIP-seq peaks that are conserved across different tissues in mice? ENCODE provides peaks for individual tissues, but I was wondering if anyone had already found common sites.
You can do it by using bedtools or homer. Download all of the bed files for CTCF ChIP-Seq peaks of different tissues in mice from ENCODE and run the command as described on the bedtools/homer web page.
You can take a look at this link: