Downloading Hi-C Data for Chromosome 9

[ashvinravi]

Hi, I'm having trouble downloading Hi-C data for chromosome 9 specifically using juicebox. When I use juicebox, it creates 2 files (chr9.KRobserved.gz. and chr9.KRNorm.gz) respectively, but both files are completely empty. Is there an alternate way I can download Hi-C data for specifically chromosome 9/has anyone else encountered this issue? I'm able to download Hi-C data using juicebox for all other chromosomes

[engreitz]

Which cell type are you looking at? If K562 cells, chr9 KRnorm might not be available due to the BCR-ABL translocation, if I recall correctly

On Fri, Feb 25, 2022 at 9:58 AM Ashvin Ravi @.***> wrote:

Hi, I'm having trouble downloading Hi-C data for chromosome 9 specifically using juicebox. When I use juicebox, it creates 2 files (chr9.KRobserved.gz. and chr9.KRNorm.gz) respectively, but both files are completely empty. Is there an alternate way I can download Hi-C data for specifically chromosome 9/has anyone else encountered this issue? I'm able to download Hi-C data using juicebox for all other chromosomes

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[ashvinravi]

Thank you for getting back to me so quickly! I am in fact looking at K562 cell type - I was under the impression that the Hi-C data was an average of 10 different cell types - is that just for the ftp://ftp.broadinstitute.org/outgoing/lincRNA/average_hic/average_hic.v2.191020.tar.gz Hi-C data? If so, what are the different cell types available to download via juicebox besides K562?

[engreitz]

please see supplemental methods of Fulco et al. Nat Genet 2019

On Fri, Feb 25, 2022 at 10:12 AM Ashvin Ravi @.***> wrote:

Thank you for getting back to me so quickly! I am in fact looking at K562 cell type - I was under the impression that the Hi-C data was an average of 10 different cell types - is that just for the ftp://ftp.broadinstitute.org/outgoing/lincRNA/average_hic/average_hic.v2.191020.tar.gz Hi-C data? If so, what are the different cell types available to download via juicebox besides K562?

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