Where can I find the .bedpe files from Roa et al 2014?

[David Katz]

On Juicebox, I am able to visualize loops and contact domains from the bedpe files produced on the Roa et al 2014 datasaet. I would like to look at those .bedpe files myself. Can someone please let me know where I can download them?

Thank you,

David

[Suhas Rao]

Hi,

You can find the loop and domain annotations here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525 (see the files labeled with the suffixes "looplist.txt.gz", "looplist_with_motifs.txt.gz", or "Arrowhead_domainlist.txt.gz". These are not exactly bedpe files but the first position columns are the same as bedpe files and these are loadable in Juicebox. 

Best,

Suhas Rao

[David Katz]

Thank you so much for your answer! I am becoming more familiar with the GSE63525 dataset. I still have some confusion. According to the readme file, the file "GSE63525_GM12878_insitu_primary_30.hic" contains the .hic matric for HIC experiments 1-29. However, when I use straw to download these 29 matrices and then add them together, the contact matrix is significantly larger than the matrix in "GSE63525_GM12878_insitu_primary_30.hic". How was  "GSE63525_GM12878_insitu_primary_30.hic" obtained from the 29 hic files?