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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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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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