Entering edit mode
6.1 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.
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