qiime feature-table filter-features within replicates

General Discussion
#1

Hello! I have a question regarding the use of

qiime feature-table filter-features

I have 4 replicates for each experimental condition from which I have extracted DNA (in triplicate) and performed 16s sequencing. So, I have a total of 12 data points her experimental condition (4 experimental replicates X 3 extraction replicates).

I noticed that there are a lot of singletons in my data and would like to filter the rarefied table. I have gone through the tutorial and it is really great in helping me filter out the singletons, but across all the samples at the same time. I was wondering if it would be possible to do the same within the 12 replicates of each experimental condition (within each group/description column, so to speak). I would really appreciate your help with the same. Thank you!

#2

Hi!
I would create a new column in a metadata file, in which all samples will be grouped according to how you want to filter them. Then it is possible to filter original for each group in this column and create numerous tables, by one for each group. Apply filtering to each table, then merge tables back in one.
If you are using Jupyter notebook and can write a small script to do it, then it is easy. But manually it looks like a lot of commands to run.

1 Like
#3

Ahh OK! I can try that…