I'm trying to normalize the coverage signals of ATAC-seq reads against its own background using normal distribution, described in this paper

It says:

Finally, all open chromatin coverage measurements were normalized by standardization to the mean and standard deviation of coverage over a set of 25,000 randomly selected background regions. To select background regions, the set of peak open regions were widened to 20,000 bp, reduced, and subtracted from the genome assembly. Thereafter, 25,000 random positions were selected and widened to reflect the distribution of widths in the set of open peaks. Coverage within these background regions was then calculated, and regions with zero coverage were discarded (~5%). The distribution of counts within background regions approximated a log-normal distribution. Mean and standard deviation of these background regions was calculated and used to transform the coverage measurements for the entire genome.

Does anyone know any existing codes doing that? I know Anshul's pipeline does that but can't find the specific script for that step.


1 Answer 1


Supplementary File 5 and 6 contain the code you're looking for.

  • 1
    $\begingroup$ Welcome to the site. Could you expand a bit more the question, explaining what does each file contain, and how are they helpful, or where in the file is the relevant information. Also if you could quote some relevant parts of the files, this answer would improve a lot. $\endgroup$
    – llrs
    Feb 14, 2018 at 7:52

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