Identification of Most Abundant Organisms

[MaryAnn (Mary)]

Thank you for your help!
Just another question, there is a way to know how much reads are responsible for my most abundant species?

[ChrisKeefe]

Hi @MaryAnn,
As for your specific question, you can use feature-table summarize to generate a feature table Visualization, then open with q2view or qiime tools view. There are three content tabs - look in the tab titled "Feature Detail". This lists features sorted by frequency.

Incidentally, qiime feature-table tabulates-seqs will let you BLAST your features, if you need to put them in context quickly.

You may want to spend some time with the methods and visualization presented in the Tutorials. They are not comprehensive, but will give you a good base for understanding what is available in QIIME 2, and where you might find it. The docs are a great resource as well.

Good luck out there!
CK

[MaryAnn (Mary)]

I already have my feature table and taxonomy but i would like to know, for example, how many reads are streptococcus responsible for?

Thank you for your reply

[Nicholas_Bokulich]

@MaryAnn

how many reads are streptococcus responsible for?

@ChrisKeefe already answered this for you:

@ChrisKeefe

you can use feature-table summarize to generate a feature table Visualization, then open with q2view or qiime tools view . There are three content tabs - look in the tab titled “Feature Detail”. This lists features sorted by frequency.

You can summarize a feature table that has been collapsed on taxonomy (qiime taxa collapse) to see total # of reads assigned to all streptococcus