Please direct your questions to Peter J. Park.
Read density files represent smoothed read density (gaussian smoothing, bandwidth=200bp), normalized for dataset size, but not yet by copy number. An additional file containing smoothed read density of genomic sequencing data is provided for copy number normalization. All coordinates are for dm3 assembly.
Note that PI/EDIs are not derived from smoothed read density, provided above, but from ratios of unsmoothed read density, as described in the methods section.