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

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