Hi, I don’t know if it is what you are looking for but you can use like a core feature and choose 90,95 or 100%, download tsv with unic names and filter your table to keep only this features.
As I understood, you want to get rid of some “noise” in your samples and leave only the reads of bacteria by your choice. If you will perform core analysis, you will find features that counted, for example, in 50%, 55% and so on to 100% of samples. You can choose the tsv file which contains the list of features, which are counted in corresponding % of your samples. You can then filter your table to remove everything from your samples except included in your list. But I am not sure what you want to do with your samples, maybe I misunderstood you
Thanks a lot, I need to remove a noisy reads from all my samples without discarding the samples, to do that do I need to filter based on seq.qza or taxonomy.qza, or table.qza?
I want to remove all sequences present in the positive and that shouldn’t be there also removing that reads from all my samples I do not know how to fix the --p-min-features threshold.
Do you think I need to use this below command?
qiime feature-table filter-samples
–i-table table.qza
–p-min-features 10
–o-filtered-table feature-contingency-filtered-table.qza
With this command you will delete all samples which contains less than 10 features. It is definitely not what you wanted to do.
If you want to delete features, not samples, you can use