Hi,
I do have relative frequency in the form of biom format from qiime2 by using the below command, I have multiple samples which belong to three groups: soil , root and shoot.
- How should I filter top10 variable phyla across these three groups in all samples and which tool should I use to make graph
qiime taxa collapse
–i-table feature-table.qza
–i-taxonomy taxonomy.qza
–p-level 2
–o-collapsed-table phyla-table.qza
Where feature-table.qza is from output of dada2/deblur and the taxonomy.qza file comes from the classifier I’ve linked above.
Now we will convert this new frequency table to relative-frequency:
qiime feature-table relative-frequency
–i-table phyla-table.qza
–o-realtive-frequency-table rel-phyla-table.qza
This new artifact now has the relative-abundances we want. To get this into a text file we first export the data which is in biom format:
qiime tools export rel-phyla-table.qza
–output-dir rel-table
Kind Regards