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picrust / picrust2

Code, unit tests, and tutorials for running PICRUSt2
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dada2 to picrust2 #135

Closed ShailNair closed 3 years ago

ShailNair commented 4 years ago

Hi, Is there any to use dada2 output (asv abundance table, taxonomy table assigned with SILVA database)directly in picrust2 or to convert the dada2 output to picrust2 compatible format? I didn't find any solid material regarding this on DADA2 and google. I have my OTU/ASV taxonomy, abundance, metadata files in txt (tsv/csv) format as well as phyloseq object (Taxonomy assigned using SILVA database).

Any help/suggestions will be highly appreciated.

gavinmdouglas commented 4 years ago

Hey @razz1618,

Yes you can certainly format the objects output by DADA2 to be compatible with PICRUSt2. You can see the expected format at the beginning of this tutorial: https://github.com/picrust/picrust2/wiki/PICRUSt2-Tutorial-(v2.3.0-beta)#tutorial-dataset

So you will need to output the ASV sequences in FASTA format and create a tab-delimited abundance table. It's not necessary to create a BIOM file - you can just create a tab-delimited table with the extension .tsv. Samples are columns and ASVs rows (first column is the ASV ids).

Best,

Gavin

ShailNair commented 4 years ago

Thanks. it seems to be working fine.

joshuacgil commented 3 years ago

Hi @razz1618, I have been trying to do the same but I have been unsuccessful and similarly I cannot find any clear instructions on how to convert my data into the proper .fna and .biom files. Can you elaborate on what you did/what needs to be done to go from DADA2 to Picrust2?

Thank you,

-josh

ShailNair commented 3 years ago

@joshuacgilPICRUST2 accepts the default DADA2 ouput of asv.fasta and count table in .tsv format (no need of .biom file). Check the link for similar issue- https://github.com/picrust/picrust2/issues/136#issuecomment-743696114