In the manuscript Hi-C maps are described at 5-, 10-, 40- and 100-kb resolution for the NPC, glia, and neuron cell types. The metadata description for contact maps accessible in the synapse databased are described as 40- and 100-kb. Where can the high-resolution 5- and 10-kb contact maps be downloaded? Thank you.

Created by Evan egeller
You're welcome, Evan! Feel free to reach out if any other questions arise.
Yes, I wanted to confirm that the shared .hic files include binning at 5- and 10-kb for use in downstream loop calling. Thank you Prashanth.
Right, those 40 and 100kb matrices were generated using HiC Pro and used for some visualization (e.g., in Fig 1 E and I) and the raw 10kb HiC-Pro matrices were used for calling interactions at schizophrenia loci (e.g., Fig 2C, D). Those are not present on Synapse. However, HiCCUPS loop calls at the higher 5 and 10kb resolutions were done using these .hic files. I think that is what Evan may be inquiring about?
I think @egeller may be referring to the description here: https://www.synapse.org/#!Synapse:syn12984505 "Binning was performed in 40kb and 100kb non-overlapping, adjacent windows across the genome and resulting contact matrices were normalized using.."
Hello, Our apologies if there was a mistake in the metadata. The .hic files actually come with the following preprocessed resolutions: 2500000 1000000 500000 250000 100000 50000 25000 10000 5000 These were the .hic contact maps used to call loops at 5 and 10kb resolutions. Hope that helps.
@rajarp01 - can you please take a look at the question above

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