How/where to obtain a bigwig or bedgraph of unmappable genome regions?
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5.5 years ago
goodez ▴ 640

I want to keep it simple. I need a track file (bigwig or bedgraph) for hg38 that only contains unmappable regions. It should look like this:

chr2  2999982 3000001   1
chr2  3000272 3000275   1
chr2  3000286 3000307   1
chr2  3000453 3000457   1
chr2  3000482 3000488   1
chr2  3000539 3000541   1
chr2  3000587 3000613   1
chr2  3000616 3000618   1
chr2  3000679 3000688   1
chr2  3000692 3000708   1

Right now my only plan is to k-merize the genome and then align it to itself. Then I would convert the alignment to bigwig and filter it for regions with no coverage. Does this type of file already exist somewhere? I'd rather avoid this process.

alignment genome • 930 views
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It's been a long time since I used gem. Are you looking for something like this? https://wiki.bits.vib.be/index.php/Create_a_mappability_track

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