I have DNA methylation bigwigs with single cytosine resolution and I am trying to reduce the size of the files by averaging the methylation values across bins. I found that bigwigCompare can take the same bigwig twice and average the signal across bins using this command:
$ bigwigCompare --operation mean -b1 wt_CG.bw -b2 wt_CG.bw -o wt_CG_bins.bw
However, methylation data is discontinuous and there may be regions with no cytosines that shouldn't be considered as having zero signal (the default behaviour of Deeptools), so I added the flag --skipNonCoveredRegions. But this gives me the following error:
$ bigwigCompare --operation mean --skipNonCoveredRegions -b1 wt_CG.bw -b2 wt_CG.bw -o wt_CG_bins.bw
[bwClose] There was an error while finishing writing a bigWig file! The output is likely truncated.
I tried using different methylation input file, and two different bigwigs for -b1 and -b2 but I got the same error.
I am not sure if this is limited to sparse data like DNA methylation, but it would be great if the --skipNonCoveredRegions worked as otherwise the methylation level is underestimated on wider regions as a lot of bins with no data in it are now zero.
Hello,
I have DNA methylation bigwigs with single cytosine resolution and I am trying to reduce the size of the files by averaging the methylation values across bins. I found that bigwigCompare can take the same bigwig twice and average the signal across bins using this command:
However, methylation data is discontinuous and there may be regions with no cytosines that shouldn't be considered as having zero signal (the default behaviour of Deeptools), so I added the flag
--skipNonCoveredRegions
. But this gives me the following error:I tried using different methylation input file, and two different bigwigs for
-b1
and-b2
but I got the same error.I am not sure if this is limited to sparse data like DNA methylation, but it would be great if the
--skipNonCoveredRegions
worked as otherwise the methylation level is underestimated on wider regions as a lot of bins with no data in it are now zero.