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tanlongzhi / dip-c

Tools to analyze Dip-C (or other 3C/Hi-C) data
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The coordinate system of SNP file. #45

Closed AIBio closed 2 years ago

AIBio commented 2 years ago

Hi Longzhi,

@tanlongzhi

I sorry to bother you again. Our approach to recording a base in the genome can be divided into two group: 0-base or 1-base. I would like to know the coordinate system used by the SNP file you provided in Github.

Best wishes~ Hanwen

tanlongzhi commented 2 years ago

Hi @AIBio, no problem at all. Glad to help! The file should be 1-based, because it's converted from VCF files (some example conversion scripts for mice can be found in scripts/snp_*.py).

AIBio commented 2 years ago

Thank you very much!