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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Metadata connections SQMtools #849

Open inej90 opened 3 weeks ago

inej90 commented 3 weeks ago

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.

fpusan commented 3 weeks ago

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.