Intersecting ENCODE datasets

Intersection is based on genomic coordinates, so the Intersect tool is found in the Operate on Genomic Intervals section. We will start with the DHS dataset, which as you can see in the history panel there are a lot of DHS sites (blue arrow). We want the overlapping intervals from the fixed and clustered SNPs returned. Make the choices as shown below then click execute.

Repeat this step using the ENCODE TFos for the intersect field.