dada2 ouput and importing sample data

[insectnate]

I am attempting to switch from using qiime2 and do things directly in R however following the dada2 pipeline I have a phyloseq obj that works but it lacks sample data. I have tried a number of solutions suggested on this and the dada2 forum to add the sample data but I get either an error that
Problem with OTU/taxa indices among those you provided.
or
Component sample names do not match.
I am using a metadata format (csv file) that has worked in phyloseq before but here there is some kind of problem with the merging of the sample data.
This is very confusing as the sample.id names match from the otu_table import and the metadata file. The phyloseq obj made from just the otu table and tax table works fine but without sample data.....

[spholmes]

Nathan One problem I have seen in sample.csv files is a # at the top which is interpreted as a comment, have you tried a smaller set also just to see if there is a strange character somewhere? Best Susan

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On Mon, Dec 2, 2019 at 2:54 PM Nathan Jones ***@***.***> wrote: I am attempting to switch from using qiime2 and do things directly in R however following the dada2 pipeline I have a phyloseq obj that works but it lacks sample data. I have tried a number of solutions suggested on this and the dada2 forum but I get either an error that Problem with OTU/taxa indices among those you provided. or Component sample names do not match. I am using a metadata format (csv file) that has worked in phyloseq before but here there is some kind of problem with the merging of the sample data. This is very confusing as the sample.id names match from the otu_table import and the metadata file. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1275?email_source=notifications&email_token=AAJFZPISF76H2ECXMJJJ3LTQWWG3NA5CNFSM4JUMLWXKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4H5POUWQ>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJFZPJF2PIXBTKC4ZWZL43QWWG3NANCNFSM4JUMLWXA> .

-- Susan Holmes John Henry Samter Fellow in Undergraduate Education Professor, Statistics 2017-2018 CASBS Fellow, Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

[insectnate]

Hi Susan,
I have looked for errant #, using unix vs mac line break invisibles, but found nothing that I tried had any effect so far on the behavior of the phyloseq merge where I try to add the sample data to the existing phyloseq object produced from the dada2 output (seqtab.nochim matrix and taxa matrix).

The weird part is I have used this sample data file successfully in phyloseq following the qiime2 to R methodology detailed by @ViridianaAvila previously.
#821

One big difference I notice is the use of the actual DNA sequence as the OTU ID.

[insectnate]

Ahhh!!! I had to transpose the otu table from dada2 and then switch taxa_are_rows to TRUE. Then the phyloseq(otu_table(nochimTable, taxa_are_rows = TRUE), tax_table(taxa), sample_data(metadata)) seems to work to give a functional phyloseq object from the dada2 pipeline output.

I used import_qiime_sample_data function to import the metadata.
Cheers,
Nathan

[spholmes]

Thanks so much for explaining how you fixed this, susan

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On Tue, Dec 3, 2019 at 2:03 PM Nathan Jones ***@***.***> wrote: Ahhh!!! I had to transpose the otu table from dada2 and then switch taxa_are_rows to TRUE. Then the phyloseq(otu_table(nochimTable, taxa_are_rows = TRUE), tax_table(taxa), sample_data(metadata)) seems to work to give a functional phyloseq object from the dada2 pipeline output. I used import_qiime_sample_data function to import the metadata. Cheers, Nathan — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1275?email_source=notifications&email_token=AAJFZPL6L2H5OF7DTMBHEQ3QW3JR3A5CNFSM4JUMLWXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEF27AMQ#issuecomment-561377330>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJFZPLD4UNTSCO3J4NKIXLQW3JR3ANCNFSM4JUMLWXA> .

-- Susan Holmes John Henry Samter Fellow in Undergraduate Education Professor, Statistics 2017-2018 CASBS Fellow, Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/