pastis-mds model with HiC contact map input

[beyzoskaya]

Can I run the pastis models with contact map txt files? I need to calculate dSCC values for chromosomes one by one and I need to get results of dSCC for different resolutions of data for HiC dataset. Is it possible to run like this or how can I run chromosome by chromosome models to calculate dSCC values?

[gesinecauer]

Hi @beyzoskaya! Apologies for the delay in responding.

Is this still something you'd like help with? If so, I have a few follow-up questions:

It sounds like you want to do the following... is that correct?

• You are seeking to use the multidimensional scaling (MDS) algorithm - not the probabilistic PASTIS algorithm
• You want to infer chromatin structures for individual chromosomes, rather than inferring a whole-genome structure
• You've binned your Hi-C dataset at a variety of resolutions, and would like to perform structural inference at each resolution.

Also, how are your contact map text files formatted?