Question

Are there mm39/GRCm39 blacklist regions?

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2.5 years ago

Ian 6.1k

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

blacklist • 3.7k views

ADD COMMENT • link updated 15 months ago by igor 13k • written 2.5 years ago by Ian 6.1k

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

ADD REPLY • link 2.5 years ago by igor 13k

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Thank, I missed that. Mysterious.

ADD REPLY • link 2.5 years ago by Ian 6.1k

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

ADD REPLY • link 2.5 years ago by cpad0112 21k

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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.

ADD REPLY • link 2.5 years ago by Ian 6.1k

score 3 · Accepted Answer · 2023-08-18

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15 months ago

Michael ▴ 30

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!

ADD COMMENT • link 15 months ago by Michael ▴ 30

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

ADD REPLY • link 15 months ago by igor 13k