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abyzovlab / CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
MIT License
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CNV for species comparative genomics #181

Open VaninaTonzo opened 1 year ago

VaninaTonzo commented 1 year ago

Hi all,

I am trying to use CNVpytor to get copy number variation between different non model species. I have one good reference genome of 1 diploid species and WGS of 9 related species.

I am following the instructions but I have a couple of questions:

  1. When I merge the CNV calls for all the species I get numbers on the deletion fields > 0, I am not sure how to interpret this table.

    Screenshot 2023-05-10 at 16 48 45

  2. how to determine the more accurate bin size? I tried 100, 1000 and 10000. This is an example with bin size 10000 Tbolo_111

  3. Do you have any suggestion about how to get and compare CNV between different species

Thanks in advance for your help,

V