Dump norm KR failed for certain resolution

[Hurley Li]

Hi, 

When I run juicebox dump norm KR on a .hic file, sometimes it failed at certain chromosome, but only at some resolution but not others. 

For instance, I have this error "Norm not available at chr14 1700 BP KR", also not available at 2000 BP, but I do successfully dumped for resolutions like 1100BP, 1200BP, 1300BP... etc. I'm not intend to use these weird resolutions, these are just for testing, but I do hope I can get norm KR at 2000BP. 

I know if the matrix is too sparse, I won't get KR at certain bin, but my data is at resolution ~2kb. Is there any specific reason that the norm KR was not available at certain resolution? My juicebox pre did not generate any error. 

Thanks in advance!

Hurley

[Neva Durand]

Hi Hurley,

The norm KR is available when the KR matrix balancing algorithm converges.  When there's no convergence, sparse rows are successively thrown out and the normalization is tried again, up to a certain point; in the final iteration, the 10% sparsest rows are thrown away and if convergence still fails, a vector of NaNs is returned.

Since it seems clear that you are comfortable making your own jar, you might want to modify how many times the normalization is attempted before it fails.  Have a look at the file juicebox.tools.utils.original.NormalizationCalculations.java, and look at the function computeKR.  You would modify the code around "iteration" to be something higher.

After modifying, instead of calling juicebox pre, you should call juicebox addNorm <hic file> with your previously created hic file.

Best

Neva

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org