Exporting DADA2 (R package) results to work with qiime2

[Jaroslaw_Grzadziel (Jarosław Grządziel)]

According to the Dada2: qiime2 virtual machine vs RStudio performance topic, especially:

@jairideout

Use DADA2 from within R or RStudio (i.e. outside of QIIME 2), save the results, and import the feature table to continue analyses in QIIME 2.

I want to ask if anybody know how exactly move from R to q2 ?
Dada2 workflow in R produces this kind of outputs:

errF and errR - the result of errors learning
derepFs and derep Rs - the result of dereplication
dadaFs and dada Rs - after sequences variants inference
mergers - merged paired reads

seqtab.nochim - the file where first column is samples list, next columns headers are sequences after chimera removal and below we can see counts, see below:

As I mentioned in previous topic I prefer using R for dada2, however I would like to taxonomy assignment in qiime2 (and other downstream analysis). Have anyone an idea how to deal with this problem ? Maybe someone is already working like this ?

Thanks

[thermokarst]

Hi @Jaroslaw_Grzadziel!

@Jaroslaw_Grzadziel

I want to ask if anybody know how exactly move from R to q2 ?

Have you had a chance to review this topic from a few months back?

Dada2 back to qiime 2

Hi All, Due to slow running time, I ran dada2 independently using R. However, I have an issue: How do I create a phylogenetic tree in Qiime2? Procedure: I saved the output of the dada2 taxa file transformed it and created a taxa table: taxat <- t(taxa)#transpose the table taxat <- cbind('#OTUID' = rownames(taxat ), taxat)#Add '#OTUID' to the header (required by biom) write.table(taxa, "dada2_taxa.txt", sep='\t', row.names=FALSE, quote=FALSE) I converted the dada2_taxa.txt into a biom table…

Let us know if that gets you moving in the right direction! Thanks!

[Jaroslaw_Grzadziel (Jarosław Grządziel)]

Thank you @thermokarst again !! I have no idea why I couldn’t find this topic.

Summing up the resolution * (thanks to @ebolyen):

• *assuming that we want to start with dada2 in R and move to taxonomy assignments and different analysis in qiime2 (e.g following q2 tutorials like Moving Pictures etc.)

1. in R
   write.table(t(seqtab.nochim), "dada2-analysis/seqtab-nochim.txt", sep="\t", row.names=TRUE, col.names=NA, quote=FALSE)

2. in R
   uniquesToFasta(seqtab.nochim, fout='dada2-analysis/rep-seqs.fna', ids=colnames(seqtab.nochim))

3. in q2
   qiime tools import \
--input-path dada2-analysis/rep-seqs.fna \
--type 'FeatureData[Sequence]' \
--output-path rep-seqs.qza

4. in q2
   echo -n "#OTU Table" | cat - dada2-analysis/seqtab-nochim.txt > dada2-analysis/biom-table.txt

5. in q2
   biom convert -i dada2-analysis/biom-table.txt -o dada2-analysis/table.biom --table-type="OTU table" --to-hdf5

6. in q2
   qiime tools import \
--input-path dada2-analysis/table.biom \
--type 'FeatureTable[Frequency]' \
--source-format BIOMV210Format \
--output-path table.qza

Once again, thank you @thermokarst and @ebolyen !!