The table does not appear to be completely represented by the phylogeny.
When I try to run the core-metric code.
But I believe I have an issue that doesn't apply to the normal root of the issue (at least from what I have seen on this forum so far). Obviously I suspected I needed to filter my rep seqs file and then make a new tree. However, that did not work. So I suspect I have feature IDs in my table that aren't present in my rep-seq files. I have merged both of these items from different studies.
If you think my hunch is correct...is there a way to filter table features by rep seq feature IDs? Basically the reverse of filtering your rep seq file by your table file if you catch my drift. I could not find anything on this.
Thank you!
Cheers,
Sam
So just to clarify... Are you saying to run --p-exclude-ids which would make a rep seq file with features NOT present in the otu table. Then I can use that file to make a list of features and then filter them out of table itself?
I would start here, by building a list of feature IDs found in the rep-seqs file. There are many ways to do this. My first thought is to extract the .qza file, then find the rep-seqs file, then use linux commands like cut to extract the IDs that are in this file.
With my 'good' IDs in hand, I would then removing all other IDs from my table like this: