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TADbit model: input matrix not generated by TADbit #350
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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 |
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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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!
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