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tanlongzhi / dip-c

Tools to analyze Dip-C (or other 3C/Hi-C) data
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Is variant masked genome ref required for the alignment ? #41

Closed yxian9 closed 3 years ago

yxian9 commented 3 years ago

Thanks for providing this awesome tool!

I just want to double-check do I need to use variant masked genome ref when doing the alignment? That's what I read in some allele-specific analysis paper. Sorry, I do not fully understand how hickit.js resolve the phrase. Thanks!

tanlongzhi commented 3 years ago

Thank you for your kind words. A variant-masked genome reference is not needed. In fact, the aligner (BWA) cannot accept N-masking information anyway.

yxian9 commented 3 years ago

Thank you for the prompt reply!