Make a taxon abundance table and beyond

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Often times you need to make a table summarizing sequence counts assigned to all taxa (rows) from all your samples (columns), similar to an OTU table. You can make this table by first running RDP Classifier on multiple sample files (FASTA) and then selecting appropriate columns and rows (using Excel or other spreadsheet tools) from the classification summary file (-h option).

Classification results from multiple samples can be combined but remain as separate columns in the count table using 'merge-count' (to combine individual count tables) or 'merge-detail' (to combine individual assignment detail files) subcommand.

The same classification summary file can be imported to R for further analyses with contextual environmental variables using Phyloseq and RDPutils (see tutorials).

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