How to decide the value of cut-off

[Jasonfengjx]

I am currently working with HiSV and have encountered some challenges. I understand that the cutoff value is crucial for the precission , but I am unsure about the best approach to determine this threshold in the context of HCC1954 and other datasets.

[Jasonfengjx]

By the way, can you directly publish your result of hcc1954 cell line.

[GaoLabXDU]

Hi Jason，

1. We believe that the cut-off setting is vary related to the sequencing depth. Here，I provided the number of contact interactions and the corresponding cut-off settings of some samples, I hope these can help you.
   When the total number of upper triangular interactions of chromosome 1 interaction matrix is 3311386，14876687 and 71569073, its intra_cutoff is set to 0.5, 0.5 and 0.6 respectively (Here, the binSize is setting to 50Kb).
   When the total number of interactions of chromosomes 1 and 22 interaction matrix is 24534, 102448 and 1093558, its inter_cutoff is set to 0.5, 0.8 and 0.9 respectively.
   (Here, the binSize is setting to 100Kb).
2. Of course we can provide the results of HCC1954. Can you leave your email and I will send it to you.

[Jasonfengjx]

Thank you for answering my question, I will try to modify the value of cut-off. And my email is 1264512262@qq.com.