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robinweide / GENOVA

GENome Organisation Visual Analytics
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Several chromosomes has error after loading the HiC file #309

Open Moonriver1988 opened 2 years ago

Moonriver1988 commented 2 years ago

Hello,

I am trying to load .hic file from 4DN(https://data.4dnucleome.org/experiment-set-replicates/4DNESI7DEJTM/), when perform pyramid analysis, I found several chromosomes have error(e.g. chr3, chr4, chr9, etc), which cannot be displayed, the error message is below. I also tried to load .mcool file but still these chromosomes have problem. But when I display .hic file with Juicebox, the coverage of these error chromosomes are very good. Could you help me with this? Thank you very much!

Error in if (head(edge$y, 1) != 0) { : missing value where TRUE/FALSE needed

Warning in min(x) : no non-missing arguments to min; returning Inf Warning in max(x) : no non-missing arguments to max; returning -Inf Error in if (head(edge$y, 1) != 0) { : missing value where TRUE/FALSE needed

teunbrand commented 2 years ago

Hi there,

When you display the data in Juicebox at the same resolution that you imported; if you set the "Norm" to something else than "None", is there still data there? Previously, we've had a few surprises with the balancing vector being absent for some chromosomes.

Moonriver1988 commented 2 years ago

Hello,

Thanks for your reply! When set to balancing in juicebox, the data cannot be displayed, but with other normalization method like coverage and coverage(sqrt) the data can be displayed, I also found different chromosomes have display problem at different resolution after balancing. When set "balancing = FALSE", all the chromosomes have the same error but juicebox can still display. I'd like to know in this case do you have any suggestion for how to do normalization in GENOVA? Thank you very much for your help!