meaning of regions not covered in UMAPM24

[Jingga Inlora]

Hi,

I asked the same question on Biostar.org (https://www.biostars.org/p/9517172/) but didn't get a response so I'm going to try it here. I downloaded the UMAPM24.bedgraph from the website and intersected it with my regions of interest to calculate the mappability score in those regions. I noticed that some regions are not covered in the UMAP bed file. Is it safe to assume that those regions are not uniquely mappable, i.e., score is 0?

Thanks for your help!

~J

[Mehran Karimzadeh]

Hello Jingga,

Yes; the Umap bed files contain genomic regions uniquely mappable by at least 1 k-mer (single-read mappability).

The Umap bedGraph and bigWig files contain the mappability score for each genomic position according to a given k-mer (multi-read mappability).

Mehran

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