Memory consumption explodes when using mappability tracks about gat HOT 4 CLOSED

Hi, typically the memory problem occurs if a workspace is provided that contains 4 BED columns where the fourth bed column is some form of label. For example::

chr1 10   100  region1
chr1  2000 3000 region2

while the intention is likely that these regions belong to the same workspace, GAT will treat these as individual and compute samples separately. This causes the memory to explode, especially if there are
many such regions. Can you please check if that is the case in your bed files you supply as the workspace? Best they should contain only 3 columns or if they contain 4, the fourth column should be identical throughout:

chr1 10  100 mappable
chr1 2000 3000 mappable

Some gat datasets are here:

https://www.cgat.org/downloads/public/gat/datasets/

I will see if we have an mm10 somewhere.

Best wishes,
Andreas

from gat.

Closing for now.

from gat.

Hi, do any of you have mm10 mappability track file somewhere that I can download?.

Any help is appreciated since it's not publicly available to my knowledge.

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