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I obtained tables running the SQM using Flye coassembly. On other hand, I have created a metadata table where I have all the information about my samples.
My question is: how can I connect tables generated by SQM and my metadata to visualize diffrences for example between farms, animal pruction system etc...? Can I obtain taxonomic results by farm instead of identification number (which I put at the beginning of the SQM analysis in my file samples) or not?
Thank you in advance.
The text was updated successfully, but these errors were encountered:
See the parameter metadata_groups in plotTaxonomy, It may do what you need.
But generally speaking SQMtools will not handle metadata, and you will need to manually pass the right information to whichever R package you are going to use for downstream analysis.
I may consider writing a wrapper that goes from SQMtools (plus an optional metadata table) to phyloseq, which would be useful since phyloseq does handle metadata.
Dear Fernando,
I obtained tables running the SQM using Flye coassembly. On other hand, I have created a metadata table where I have all the information about my samples.
My question is: how can I connect tables generated by SQM and my metadata to visualize diffrences for example between farms, animal pruction system etc...? Can I obtain taxonomic results by farm instead of identification number (which I put at the beginning of the SQM analysis in my file samples) or not?
Thank you in advance.
The text was updated successfully, but these errors were encountered: