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Hello, I want to ask where should I download refs (①star_index: /share/home/zliu/share/Data/public/ref_genome/mouse_ref/M23/RNA_snp_split/CAST_B6_star_index; ②snp: /share/home/zliu/share/Data/public/ref_genome/GRCm38/snp/Tan.CAST_B6.snp.GRCm38.withchr.txt; ③par: /share/home/zliu/share/Data/public/ref_genome/GRCm38/raw_data/par.bed; ④RNAsnp: /share/home/zliu/share/Data/public/ref_genome/mouse_ref/M23/RNA_snp_split/all_SNPs_CAST_EiJ_GRCm38.txt.gz) in config.yaml, thank you very much.

Hi Zhiyuan，I hope this message finds you well. I am writing to inquire about the processing methodology used to obtain the results presented in Fig1D of the paper "Linking genome structures to functions by simultaneous single-cell Hi-C and RNA-seq."
In my analysis, I employed a 1Mb resolution for the Hi-C data and calculated the scAB value based on contacts and 1Mb CpG frequency. Subsequently, I performed rank normalization, yet the obtained results did not effectively segregate cell types as depicted in the paper (Figure 1).

Figure 1

I am eager to delve into the details of how the data was processed in this context. Could you kindly provide insights or specifics regarding the data processing steps carried out to achieve the outcomes presented in Fig1D?
Thank you very much for your time and consideration. I am looking forward to your valuable guidance.