I am looking for a software package, or R script for generating the coordinates for a heat map of repeat density. I have a repeat library, and a table of repeat locations (via RepeatMasker), but there is some overlap between repeats. Are there any good programs that can do this? My goal is to incorporate this into a circos plot.
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If you convert your table of repeats into BED format, you can use BEDtools to count up the overlaps in bins across the genome. I created BED files tiled across the genome in whatever increments I wanted for the Circos plot, then used BEDtools to count up the BED features within each bin. Depending upon the detail you need, you can either use coverageBed or "intersectBed -c" to calculate the overlap counts per tile. BEDtools is also blazing fast.
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