I am trying to have a taxonomy barplot/ bar chart showing only the relative abundance >1% at the genus level with only the top 5 genera.
I have followed the steps shared in various discussions in the form and I am not able to produce that.
First >>> collapse the table
qiime taxa collapse
Note: this input (table_2k.qza) obtained from (qiime feature-table filter-samples)
THEN >>> convert to relative abundance
qiime feature-table relative-frequency \
Note: NO filter (p-min-frequency or --p-min-samples)
THEN >>> filter to <1% in at-least 10% of the samples.
Then, I took the collapse table (uniform_table.qza) and I run this:
qiime feature-table filter-features-conditionally
After that, I am stuck, I am not sure how to generate the barplot/ bar-chart showing the relative abundance of >1% at the genus level with only the top 5 genera.
I am not sure if what I did is correct or even makes sense.
Do I need to take the file (filtered_relative_frq_6_table.qza) and generate a new (tazonomy.qza) using qiime feature-classifier classify-sklearn ?
Thank you for all the help!