Diploid genome structure

[jinlizhang200706]

Hi pastis developer,

is it possible to used pastis-NB infer diploid genome 3d structure?

Thanks

[gesinecauer]

Hello, thanks for your question! PASTIS-NB was designed for haploid genomes and is not suitable for diploid data (unless, of course, each contact count has been phased on both ends).

You can, however, use our diploid PASTIS algorithm, which is based on a Poisson model in addition to two constraints. We do not currently have much documentation for the Poisson-based diploid PASTIS method, but this is a work in progress. If you are interested in trying it, I can provide instructions on how to use the code.

I should also mention that we are currently working on a manuscript that describes an improvement to the diploid PASTIS method, and the associated code will be made available in the next few months.

[hanshanmengqi]

Hello @gesinecauer,

I would like to know if you have released a diploid PASTIS version.

Best,
Han