Skip to content

Human's raw data file format from .cool to .mcool #2

@wy52940

Description

@wy52940

When I try to use "cooler zoomify --balance filename.cool" to convert .cool files into .mcool files, I met the error: "INFO:cooler.balance:variance is nan". I think it's the reason why I got this result after I ran PrepareData_linear.py:
The test target length is:torch.Size([970, 1, 64, 64])
tensor([[nan, nan, nan, ..., nan, nan, nan],
[nan, nan, nan, ..., nan, nan, nan],
[nan, nan, nan, ..., nan, nan, nan],
...,
[nan, nan, nan, ..., nan, nan, nan],
[nan, nan, nan, ..., nan, nan, nan],
[nan, nan, nan, ..., nan, nan, nan]])

The test data length is:torch.Size([970, 1, 64, 64])
tensor([[nan, nan, nan, ..., nan, nan, nan],
[nan, nan, nan, ..., nan, nan, nan],
[nan, nan, nan, ..., nan, nan, nan],
...,
[nan, nan, nan, ..., nan, nan, nan],
[nan, nan, nan, ..., nan, nan, nan],
[nan, nan, nan, ..., nan, nan, nan]])

And I cannot perform other pretrain .py files which need call PrepareData_linear.py.
So could I ask what kind of preprocessing steps have you performed on cell1(2,3)_10kb_contacts.cool to handle this NAN value.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions