Absolute read count after classification

[Saptarathi_Deb]

Hello Qiime users,

I wanted to know if there is any straight forward way to get absolute read count per taxa, just like the relative abundance table.
I am a little confused about how the relative abundance table is calculated? is it just based on percentage? or some other normalization method is being used.

Thank you for your support!!!

[SoilRotifer (Mike Robeson)]

Hi @Saptarathi_Deb,

It is unclear what you are asking. Your title specifies absolute read counts, yet your questions refer to relative abundance.

The raw read counts (it is actually difficult to determine absolute abundances with sequencing data) are what reside in your DADA2 or deblur feature-table output. If you want relative percentages, then you can run qiime feature-table relative-frequency. The calculation is described in the help text, i.e. add --help to the end of the command like so: qiime feature-table relative-frequency --help.

If you want to merge your features by taxonomy, check out qiime taxa collapse.