Different number of loops on GM12878 Hi-C map

[koszullab]

Different number of loops on GM12878 Hi-C map

[cmdoret]

Hi @zhang-jiankun,

Thanks for your interest. I now realize the text is confusing. Both figures are obtained with default parameters, but 18,839 was obtained on the recent Arima dataset from Ghurye et al. (ref 36 in the sentence) whereas 37,955 was obtained on the Rao et al. dataset.

The reason for this large difference is that the Rao et al. dataset is 10 times (!) more highly covered (but also more noisy) than the recent Arima dataset. Looking back, it would have made more sense to use exclusively Rao et al. for all comparisons. Logically, we should have used the same figure (37,955) in the second sentence. Thanks for raising this issue !

Best,
Cyril

[zhang-jiankun]

Hi Cyril,

Thanks for clarifying that.

Best,
Jiankun