Are there mm39/GRCm39 blacklist regions?
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6 months ago
Ian 5.9k

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

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Thank, I missed that. Mysterious.

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

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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.

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