allele mode with SNP information of a region in chr6

[ZHIDIHUAYUAN]

Hi, I am intersected in a region in chr6 and I only have the SNP information in this region. Can I used the allele-specific mode to study the differences of contacts between two alleles in this region? Should I run HiC-pro with the SNP file and keep only the the sub-matrix containing the region I am interested in?

Thank

[nservant]

Hi, If you only have the SNPs on chromosome 6, all other contacts will be classified as non allele specific ... But you should still have all valid contacts, including those which are allele specific and the other ones. In theory, in G1/G2 valid pairs files, you should only have contacts on the chr6. Best

[ZHIDIHUAYUAN]

Hi， Thanks for your help. Because I am really only interested in the interaction between A and other regions, and I don't care about the interaction between other regions and other regions. But considering that the interaction between other regions and other regions is 0, can the matrix I get be used for KR normalization? Best wishes

[nservant]

Just to be sure to understand. Which protocol are you using ? is it capture-Hi-C ? In this case, you could specifiy your capture in the config file, so that HiC-Pro will restrict the analysis to this region ?

[ZHIDIHUAYUAN]

Hi， In fact, my goal is to analysis the differences between the two alleles in MHC region. The data I have are sequences of two haplotypes assembled by myself in this area. The Hi-C data was downloaded from GEO, and I am sure it is not capture Hi-C. I want to get the contact information about this region from the HiC-pro alllele mode, but I meet with some problem when normalizing? Should I try some 5C standardization methods？ Thanks

[ZHIDIHUAYUAN]

Can I conduct the normalization by chromsome(or MHC?) and not by genome-wide?

[nservant]

Yes I guess, but by hand (HiC-Pro cannot do that for you)