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Hi,
I recently worked on multiple cool files between GENOVA and HiCExplorer.
I first converted the matrix file from raw hic-pro format to cool file without Normalizing,
Then i use HiCExplorer's hicNormalize and hicCorrectMatrix (--correctionMethod KR),
what i did using hicNormalize is this:
then what i did using hicCorrectMatrix (--correctionMethod KR) is this:
so i now have mcool files normalized using KR amongst multiple samples,what i confused is how do i set some of these parameters
1,do i need to set scale_bp=NULL which was mentioned in #356,
2,do i need to set balancing=FALSE cause i see description "
balancing | TRUE (default) will perform matrix balancing for .cooler and KR for.hic."
but i have already done KR normalizing to mcool files ?
Or are there any other Settings I need to be aware of
Thanks a lot,
Best
The text was updated successfully, but these errors were encountered:
Hi,
I recently worked on multiple cool files between GENOVA and HiCExplorer.
I first converted the matrix file from raw hic-pro format to cool file without Normalizing,
Then i use HiCExplorer's hicNormalize and hicCorrectMatrix (--correctionMethod KR),
what i did using hicNormalize is this:
then what i did using hicCorrectMatrix (--correctionMethod KR) is this:
so i now have mcool files normalized using KR amongst multiple samples,what i confused is how do i set some of these parameters
1,do i need to set scale_bp=NULL which was mentioned in #356,
2,do i need to set balancing=FALSE cause i see description "
balancing | TRUE (default) will perform matrix balancing for .cooler and KR for.hic."
but i have already done KR normalizing to mcool files ?
Or are there any other Settings I need to be aware of
Thanks a lot,
Best
The text was updated successfully, but these errors were encountered: