Are there mm39/GRCm39 blacklist regions?

Question

[Ian]

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

[igor]

There is an open issue about it: https://github.com/Boyle-Lab/Blacklist/issues/25

[Ian]

Thank, I missed that. Mysterious.

[cpad0112]

There are black listed regions for mm10 (GRCm38). See if you can use liftover from it.

[Ian]

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.

Answer 1

[Michael]

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!

[igor]

The author mentioned it on the Boyle Lab blacklists GitHub: https://github.com/Boyle-Lab/Blacklist/issues/25