Request: Could you please create a blacklist file for the latest mouse genome version (GRCm39)?

[TakacsBertalan]

[jluebeck]

Hi, I am also wondering if there are any plans to generate the blacklist file for GRCm39? Thank you!

[ey04]

Liftover is able to convert coordinates between genomes, here's the output doing the mm10-blacklist.v2.bed file to mm39, just change the extension back to bed. Some coordinates were unable to convert due to differences between the references. mm10-blacklist.v2.Liftover.mm39.bed.txt FailedLiftoverCoord.txt .

[igordot]

Is LiftOver an appropriate solution? Since this is an updated build, some of the problematic regions were resolved and others may have been introduced.

[IanCodes]

Is the mm39 blacklist planned, or has it been decided it is not necessary?
Thank you.

[serge2016]

Same question! Thank you!

[VictorGoitea]

Hi @adadiehl @aboyle
Is this not done yet? Best

[liddelowlab]

I think we received this in error.

Best,

On Tue, Aug 16, 2022, 5:51 PM Victor Enrique Goitea < @.***> wrote:

Hi @adadiehl https://github.com/adadiehl @aboyle https://github.com/aboyle Is this not done yet? Best

— Reply to this email directly, view it on GitHub https://github.com/Boyle-Lab/Blacklist/issues/25#issuecomment-1217206011, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQDW7UIFY5QHHQEC65PMFYDVZQEOBANCNFSM5C22PT4A . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[christiane-morecock]

Hi all in this thread,

I'm new to this space professionally, and would like to know what did you all decide to do in the absence of an mm39 blacklist?Did you all generate a liftover of the blacklisted regions? Or did you align to mm10 instead? I realized many downstream visualization and QC packages have mm10 as the default annotation - and require generating custom mm39 annotations. Which did you decide was a better solution and why?

Is LiftOver an appropriate solution? Since this is an updated build, some of the problematic regions were resolved and others may have been introduced.

[IanCodes]

Hi @christiane-morecock, In the end I 'liftedOver' the mm10 file to mm39, using the file from 'https://github.com/Boyle-Lab/Blacklist/blob/master/lists/mm10-blacklist.v2.bed.gz'. I used a min ratio setting of 0.95 in liftOver. Admittedly, it isn't perfect solution, but I had already committed myself to the latest version.

[mdozmorov]

If still relevant, we generated sets for mm39, as well as for T2T, using the Blacklist software. https://github.com/dozmorovlab/excluderanges