Accessing high resolution (<5kb) .hic files

[Luli Zou]

Hi,

I noticed that when viewing certain .hic files with large numbers of reads (e.g. "K562 in situ Hi-C experiment" from ENCODE) in Juicebox, a number of higher resolutions are available, down to 100bp. However, when downloading these .hic files manually, the highest resolution is only 5kb, which I recognize is a default that works well for most experiments. Is there any way to access the higher resolution files which are used for the Juicebox browser, specifically e.g. the K562 combined 500bp resolution matrix, besides processing them manually from the raw reads?

Thank you,

Luli

[Muhammad Shamim]

If you download a .hic file, all the resolutions are included in it.

My guess is that you are downloading the files aligned to hg19, which were only built to 5kb.

The files built for hg38 are built to higher resolutions.

[Luli Zou]

Thanks for your reply! I was able to find it. For others looking: https://www.encodeproject.org/experiments/ENCSR545YBD/