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wangjr03 / FLAMINGO

MIT License
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Mapping the 3D structure of all chromosomes of the whole genome #3

Closed shenlinyong closed 2 years ago

shenlinyong commented 2 years ago

The software you have developed is very perfect and useful. But I am a little confused, the chr_name parameter is mandatory if I want to build all chromosomes in the genome to a 3D result model, not just one chromosome. What should I do again?

haowang0508 commented 2 years ago

Hi, Thanks for using our software. Yes, the chr_name parameter is mandatory since FLAMINGO reconstructs the chromosome structure only based on the intra-chromosome contacts. If you want to reconstruct the 3D structures of all chromosomes, you will need to run the code on each chromosome separately and provide it to the chr_name parameter (e.g. chr_name=chr1, chr_name=chr2, etc). The current version of the code does not provide a functionality to reconstruct the 3D structures of all chromosomes altogether.