Hello, and thank you in advance for your time. I am using QIIME2-2019.4 version on a conda platform.
In summary: I am looking to properly import a .tsv feature table into Qiime2, after I manually remove taxa (features) from my negative controls present in my samples. When I view my imported table in Qiime2 viewer, the tab “Interactive Sample Viewer” contains taxa identification (k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;s__veronii), and the tab “Feature Detail” contains my sample identification and corresponding frequencies. Due to this content switch, qiime can’t pair my metadata to my feature table anymore.
In detail: I created a relative abundance plot containing all my samples (negative controls included), and within Qiime2 view, I downloaded the .csv file of the taxa and corresponding abundances present within my samples. Within the .csv file, I manually removed the taxa present in the negative controls from the samples (if also present). For example: if taxa A occurred within my negative control 500 times, and in a sample 700 times, I would subtract 500 from 700, and 200 would be the “adjusted” abundance within the sample. After completing this for all my negative controls and samples, I deleted the negative controls, keeping only my samples and their adjusted feature abundances.
Using google sheets, I converted this .csv file to .tsv, and converted the file to .biom hdf5 file:
> biom convert > -i feature-table.tsv > -o feature-table.biom > --table-style="OTU table" --to-hdf5
I then imported the .biom file into qiime as a .qza file:
> qiime tools import > --input-path feature-table.biom > --type 'FeatureTable[Frequency]' > --source-format BIOMV210Format > --output-path feature-table.qza
To view this file, I converted it to .qzv:
> qiime feature-table summarize > --i-table feature-table-final.qza > --o-visualization feature-table.qzv
When visualized with the Qiime2 viewer, the file
feature-table.qzv shows the taxa identification as the “Interactive Sample Detail” and my samples as “Feature Detail”. This mix-up halts any further use of this data file for diversity analyses.
Could anyone provide advice for me and my analysis?