Why are there regions missing from mappability tracks provided by UCSC?
To get the mappabiity tracks, I downloaded them from the link provided by UCSC (http://hgdownload.soe.ucsc.edu/gbdb/hg38/hoffmanMappability/). The file used for the analysis was k100.Umap.MultiTrackMappability.bw. Once downloaded, this was converted from bigWig to Wig using the bigWigtoWig tool from UCSC and then from Wig to bed using wig2bed from the BEDOPS suite of tools. However, upon looking at the final bed file of mappability scores, some regions are inexplicably missing. Does anyone have any idea why this is?
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jparker4 •
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I presume these are stretches of
Nsin the reference.