mm10 files in data_repo are missing

[danielagerovska]

First, thank ou very much for expanding AA to the use of mouse data!

I downloaded the reference data from https://drive.google.com/drive/folders/18T83A12CfipB0pnGsTs3s-Qqji6sSvCu but the directory does not contain any mouse reference data. Do you plan to upload it soon ?

[jluebeck]

Hi,

Thanks for reaching out, you are correct - the data repo files for mm10 haven't been released yet since we are still doing testing on our end. Unfortunately testing datasets are less abundant for mouse than for human. We hope to officially release it in the next month or so. If you (or anyone else reading this) is interested in testing it before the release, please email me at jluebeck [at] ucsd.edu and I will share the working version of the data repo. We are especially interested in testers who have samples with ecDNA or other focal amplifications. In return it would be great if we could then take a look at the resulting AA output files once completed to ensure that everything is as expected.

Thanks! Jens

[acticu]

Hi Jens,

Thank you for your tools on ecDNA amplicon investigation!

I am wondering if any updates in terms of the mouse reference data. I have already sent you an email regarding the reference data request.

Kind regard, Haobin

Hi,

Thanks for reaching out, you are correct - the data repo files for mm10 haven't been released yet since we are still doing testing on our end. Unfortunately testing datasets are less abundant for mouse than for human. We hope to officially release it in the next month or so. If you (or anyone else reading this) is interested in testing it before the release, please email me at jluebeck [at] ucsd.edu and I will share the working version of the data repo. We are especially interested in testers who have samples with ecDNA or other focal amplifications. In return it would be great if we could then take a look at the resulting AA output files once completed to ensure that everything is as expected.

Thanks! Jens

[jluebeck]

Hi @danielagerovska and @acticu,

Apologies for the delays on this, I didn't have time to take care of this before the holidays. I have made the mm10 data repo available in the README. Please let me know if there are any questions or you run into any issues.

Thank you, Jens

[danielagerovska]

Dear Jens,

Thank you for you email. I looked for the mm10 reference but it does not look to be there yet.

Maybe I am not looking in the right place. Could you be more specific about the address?

Thank you very much,

Daniela

January 7 2022 8:24 PM, "Jens Luebeck" wrote: Hi @danielagerovska (https://github.com/danielagerovska) and @acticu (https://github.com/acticu),

Apologies for the delays on this, I didn't have time to take care of this before the holidays. I have made the mm10 data repo available in the README. Please let me know if there are any questions or you run into any issues.

Thank you,

Jens

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[jluebeck]

Hi Daniela,

Sorry for the confusion, the mm10 repo is hosted through AWS and can be found on the Readme as a hyperlink.

Thanks! Jens

[acticu]

Dear Jens. I am sorry if there is anything wrong but I checked through the readme file thoroughly but didn't got the link on the Readme.md in the prepareAA directory. Could you please figure that out?

Thank you Haobin Ren

[jluebeck]

Hi Haobin,

I have made the mm10 link available in the README of my fork of AA. The link is now also available in the README of PrepareAA (see Prerequisites section) and I am also including it directly here.

Thanks, Jens