QIIME 2 is running beautifully on my virtual box and I just completed the Moving Pictures Tutorial …
Now I want to repeat this using my data which consists of non-barcoded paired-end demultiplexed fastq files (R1/R2) which have been quality filtered using QIIME 1 by my sequencing facility.
I now have a normalised and filtered .biom file which I succesfully imported using
All good so far…at this stage the only artefact I have from my BIOM is:
feature-table.qza
But to continue with phylogenetic diversity analysis I need FeatureData[Taxonomy], presumably I can get this from my a taxonomy .tab file provided with the initial .biom file. ?
If so, how would I import a tab file and what format (column heading) should it be in?
For the phylogenetic analyses, you’ll need to provide or generate a phylogenetic tree using FeatureData[Sequence]. While taxonomy and phylogeny are related, they aren’t 1-1 and the taxonomy does not include estimates of divergence. In the moving pictures tutorial, the phylogeny is estimated here using a de novo reconstruction from the sequence fragments. However, your trajectory here will depend on how the FeatureTable[Frequency] was constructed. If the table was produced using closed reference OTU picking in QIIME1, then you should be able to import the existing reference tree as Phylogeny[Rooted] and provide that to downstream analyses. Similarly, if the OTUs were assessed using open reference OTU picking, then you can import the existing rep_set.tre file as Phylogeny[Rooted] and proceed.
I finally worked it out and I was able to complete the moving picture tutorial steps using my own data
Maybe my approach is slightly convoluted but it appears to work, here is what I did:
For FeatureData[Sequence] I created a spreadsheet in excel consisting of two columns OTU IDRepSeq, saved as tab-delimited rep_seq.txt then converted to FASTA and saved as rep_seq.fna.
