Hi,

Excuse me. I am doing a project about TAD boundaries using scm3C-seq data of brain tissue. I can't search your cell-type identification results. Can you send me clusters and cell-type identification results by different ways (DNA methylation or chromatin interaction) in Fig5(a-c) of your paper "Simultaneous profiling of 3D genome structure and DNA methylation in single human cells". my email is [email protected]

Thanks very much!
Yusen

Hello,

I have been trying to reproduce the results from Figure 5c in the paper (https://www.nature.com/articles/s41592-019-0547-z/figures/5) using the final few lines in the clustering script and I have been unable to get any sort of positive clustering results using scHiCluster.

I followed the scHiCluster preprocessing steps as outlined in their repo: https://github.com/zhoujt1994/scHiCluster

Yet when I try running any of the scHiCluster functions (hicluster_gpu, hicluster_cpu, raw_pca) the embeddings seem practically random:

Could you please clarify the preprocessing steps used before feeding the data into scHiCluster and would you be able to include some of the supplementary files needed to reproduce the results in the paper?