I want to use Piphillin to get some pathway information. The server requires an OTU abundance table in csv format (see example here: https://piphillin.secondgenome.com/Samples/ExampleOtuTable.csv) and a representative sequence file in fasta format (see example here: https://piphillin.secondgenome.com/Samples/ExampleRepSeqs.fasta).
How can I get these 2 files from Qiime2?
You can use the export/extract tools to get the data you want from the output of your denoising/OTU picking methods or simply use your preferred unzipping tool on the .qza files of your choice and find what you need in the
data folder. For example after running dada2 you will have a feature-table.qza and rep-seqs.qza. The feature-table will be the equivalent of the OTU table you are seeking in biom format. You’ll have to convert that to a csv file first which you can do using the biom tool already pre-installed alongside qiime2. As for the rep-seqs.qza, the underlying file is already a .fasta file so you can probably use that just as is.
Note, I’ve never used piphillin so I can’t speak with regards to what their exact format requirements are so you might have to play around a bit with the precise formatting.
As an FYI, if you rather not go outside of qiime2, there is a q2-picrust2 plugin already available that can also do genome predictions, might be worth checking out.
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