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songweizhi / MetaCHIP

Horizontal gene transfer (HGT) identification pipeline
GNU Affero General Public License v3.0
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About the interpretation of the results #33

Open maocheng2020 opened 2 years ago

maocheng2020 commented 2 years ago

Hello! I want to ask a question about the biological interpretation of horizontal gene transfer. I used MetaCHIP to get the genes that had a horizontal transfer between MAGs. The resulting genes are annotated into a database by DIAMOND blastp. What puzzled me was the discovery that gene A( carbon fixation Mcr) had a high rate of horizontal gene transfer between members within the same class , while gene A was not detected in MAGs. I don't know if it's a bug in the program of MetaCHIP or something else, is my result reliable? Thanks!

songweizhi commented 2 years ago

Hi maocheng2020,

Thanks for using MetaCHIP, I am not sure what do you mean by saying "while gene A was not detected in MAGs". May I know how do you determine the existence of gene A in MAGs?

Best, Weizhi

wangshuya2022 commented 1 year ago

Hello! I want to ask how to know whether there is ARG in the gene on Contig that has horizontal gene transfer after finding out that MAG carrying ARG has horizontal gene transfer through MetaCHIP. Thanks!