Don't understand windows_size parameter in tadtool tad

[rachelzhu123]

hello,
i'm using tadtool to find tads. But I didn't understand window_ size and cutoff parameters. For example, I have a matrix with a resolution of 40KB, 1479 × 1479. How should I set up window_ size and cutoff parameters? Are these two parameters required?

Please help me.

thank you

[rachelzhu123]

An example command line will help me. Looking forward to your reply.

[kaukrise]

Hey,

have you looked at the README here? https://github.com/vaquerizaslab/tadtool

It contains all the information you require, including example commands. The window size and cutoff parameters are estimated using tadtool plot. If there is something unclear in the documentation, let me know.