Hi @JenKelly, It sounds like you want to filter by % on a per-sample basis (as opposed to % of all sequences). That functionality is still outstanding, as shown in this feature request. We will update you here when that feature is available.
Thank you for your replies. Yes I am interested in filtering by % on a per-sample basis. Would a work around be possible as follows; convert table to relative frequencies, identify features below a certain relative frequency (of each sample), and then remove those from the original count table?
Firstly is it possible to filter features from a relative frequency table? And if so, how could I grab the feature names of those low abundance features?
This would still not be per-sample filtering. It would only filter features that are less than a certain proportion in ALL samples, which you can do already without converting (figure out total # of reads and filter features that are observed less than some % of total reads).
If you want to filter on a per-sample basis, my guess is that you want to do this for plotting purposes. Is that correct? If you can describe the downstream goal I may be able to help guide you on an alternative route.