Hi,
Thank you for developing and sharing this useful tool. I would like to clarify how to properly use the output for downstream diversity analyses.
Specifically, I am planning to compute alpha diversity metrics (e.g., Shannon, Simpson) but am unsure which output table should be used. Should alpha diversity be calculated directly from the provided OTU table, or is there a recommended abundance matrix (e.g., normalized counts or a specific feature table) for this purpose?
In addition, the OTU table appears to include multiple genes per entry. Does each row correspond to an OTU regardless of gene identity, or should a specific marker gene be selected to define OTUs for ecological diversity analyses?
Any clarification on the recommended practice would be appreciated.
Best regards.
Hi,
Thank you for developing and sharing this useful tool. I would like to clarify how to properly use the output for downstream diversity analyses.
Specifically, I am planning to compute alpha diversity metrics (e.g., Shannon, Simpson) but am unsure which output table should be used. Should alpha diversity be calculated directly from the provided OTU table, or is there a recommended abundance matrix (e.g., normalized counts or a specific feature table) for this purpose?
In addition, the OTU table appears to include multiple genes per entry. Does each row correspond to an OTU regardless of gene identity, or should a specific marker gene be selected to define OTUs for ecological diversity analyses?
Any clarification on the recommended practice would be appreciated.
Best regards.