How to define the nchr for the pipeline

zengxiaofei / HapHiC

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

https://www.nature.com/articles/s41477-024-01755-3

BSD 3-Clause "New" or "Revised" License

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How to define the nchr for the pipeline #19

Closed chenzixi07 closed 7 months ago

chenzixi07 commented 7 months ago

Hello HapHiC developers,

I am handling a species with ~46 chromosomes.According to our previous HiC result, this species seems to be a Triploid. However, we also found that some clusters maybe diploid on the HiC heatmap. We are not quite sure at this moment. So, how should I define the 'nchr' while run the HapHiC pipeline？Should I use 46*3=138？

Regards, Zixi

zengxiaofei commented 7 months ago

Hi Zixi,

I'm not quite sure about your description. If 46 is the haploid chromosome number (karyotype: 2n = 3x = 138), and your genome assembly is haplotype-phased (e.g., p_utg or catenated hap.p_ctg), the nchr parameter should be set to 46 3 = 138.

Best, Xiaofei

chenzixi07 commented 7 months ago

Thanks for your reply, I will try.