Understanding Variants Contact Matrix
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Bapai Mallik
May 2, 2026, 10:32:41 AM (2 days ago) May 2
to 3D Genomics
Hi,
I am looking for a resource that can explain how to use the VARIANTS CONTACT MATRIX on juicebox, like the one available here on the HiC interface that comes up from the encodeproject dataset on HiC in PC3 cells. This is the page https://aidenlab.org/juicebox/?juicebox=%7BhicUrl%3Dhttps%3A%2F%2Fwww.encodeproject.org%2Ffiles%2FENCFF222UAD%2F%40%40download%2FENCFF222UAD.hic%7D For example, I am unable to understand the difference between the chromosome and assembly options. In short, I am looking for some resource that can explain the variants contact matrix, like the way the general contact matrix is described on the juicebox tutorial here https://aidenlab.gitbook.io/juicebox/juicebox-web. Can anybody please help me with this
I am looking for a resource that can explain how to use the VARIANTS CONTACT MATRIX on juicebox, like the one available here on the HiC interface that comes up from the encodeproject dataset on HiC in PC3 cells. This is the page https://aidenlab.org/juicebox/?juicebox=%7BhicUrl%3Dhttps%3A%2F%2Fwww.encodeproject.org%2Ffiles%2FENCFF222UAD%2F%40%40download%2FENCFF222UAD.hic%7D For example, I am unable to understand the difference between the chromosome and assembly options. In short, I am looking for some resource that can explain the variants contact matrix, like the way the general contact matrix is described on the juicebox tutorial here https://aidenlab.gitbook.io/juicebox/juicebox-web. Can anybody please help me with this
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