TADbit model: input matrix not generated by TADbit

[liezeltamon]

Hi,

I'm planning to repurpose this command to model a whole chromosome using a square matrix of values (not Hi-C data). Should I just provide the PATH to a text file of the square matrix (--input_matrix)?

Also, can you please point me to a resource to understand the parameters being optimised i.e. -maxdist, -upfreq, -lowfreq and -scale so I can choose sensible values especially that I'm not using Hi-C data.

Thank you!

[david-castillo]

Hi,

For a squared matrix just provide the path with --input_matrix as you said.

Have a look here http://3dgenomes.github.io/TADbit/tutorial/tutorial_10-Modeling_parameters_optimization.html to understand the parameters.

Depending on the resolution modelling a full chromosome will be impossible in terms of memory. TADbit model is intended to tackle smaller regions.

Regards

David

[liezeltamon]

Dear David, Thank you for the reply. It might be difficult then since I'm planning to model chr 1 with 6232 beads. Best, Liezel

…

On Wed, Sep 8, 2021, 18:44 david-castillo ***@***.***> wrote: Hi, For a squared matrix just provide the path with --input_matrix as you said. Have a look here http://3dgenomes.github.io/TADbit/tutorial/tutorial_10-Modeling_parameters_optimization.html to understand the parameters. Depending on the resolution modelling a full chromosome will be impossible in terms of memory. TADbit model is intended to tackle smaller regions. Regards David — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#350 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKZEDTLLSKS6OUQIPBGQUCDUA447RANCNFSM5DIYHFDQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.