The author mentioned it on the Boyle Lab blacklists GitHub: https://github.com/Boyle-Lab/Blacklist/issues/25
Are there mm39/GRCm39 blacklist regions?
Hello, have blacklist regions been created for the mm39 / GRCm39 reference genome? My search of Google and the sites below have drawn a blank. Thank you.
Sites looked at:
https://sites.google.com/site/anshulkundaje/projects/blacklists
https://github.com/Boyle-Lab/Blacklist
1 answer
https://academic.oup.com/bioinformatics/article/39/4/btad198/7126418 This paper just came out that made GRCm39 forbid lists (among others) and curated them all as a GRanges data package. I was just looking for this exact thing and happened to find this so I figured I'd share!
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There is an open issue about it: https://github.com/Boyle-Lab/Blacklist/issues/25
Thank, I missed that. Mysterious.
There are black listed regions for mm10 (GRCm38). See if you can use liftover from it.
That is a reasonable suggestion and I have made my own liftOver. I figure if 95% of the sequence overlaps then they are a good place holder. Hopefully there will be an official release.