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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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SQM to Phyloseq #732

Closed megberryman closed 10 months ago

megberryman commented 1 year ago

Do you have a suggested method for converting the taxa abundance file to a phyloseq object?

fpusan commented 1 year ago

Nuneric matrices can be found under SQM$taxa. Eg SQM$taxa$phylum$abund for the number of reads assigned to each phylum per sample. From there It should be reasonably straightforward as per https://joey711.github.io/phyloseq/import-data