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czbiohub-sf / MIDAS

Metagenomic Intra-Species Diversity Analysis (MIDAS)
MIT License
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Use bining data as ref-genome #104

Closed BaylorLyu closed 1 year ago

BaylorLyu commented 1 year ago

Thanks for you remarkable work. I use midas2 to analyze CNV，but i found that not all the sample can detect CNV. So i want to use my data after bining as ref-database, is that feasible for CNV analyze？

zhaoc1 commented 1 year ago

Thank you for being interested in MIDAS2.

"Not all the samples can detect CNV" Have you tried to lower the --select_by and --select_threshold to lower the threshold of selecting species for CNV.

"i want to user my data after binning as ref-database, is that feasible" Yes, it is feasible. However let's clarify the goal of CNV here. CNV is for species-level pangenome, instead of collection of repgenomes for the species of interest. And there are two precomputed MIDASDB: UHGG and GTDB. I think it might worth investigating the reason some samples don't have CNV results. My guess is most of species in your sample is low abundant, and didn't pass the --select_threshold filter.

BaylorLyu commented 1 year ago

Thanks for you reply.