I have looked in the qiime2 forum but no answers have been able to help me yet.
I have 27 samples. I want to extract the rep seqs from one specific sample so I can BLAST them and compare to an isolate I have from this sample's same sampling site. I seem to be repeatedly misunderstanding how I can do this.
So far I have seen these posts:
But they either weren't specific enough for what I am trying to do or weren't helpful enough for me (I'm new to QIIME2 btw).
So far I have tried creating a simplified metadata file with only the sample ID of the sample I want to retain, and then I tried using that simplified metadata file in filter-seqs against the OG repseqs from deblur:
But i received the error: Plugin error from feature-table:
All features were filtered out of the data.
Debug info has been saved to /tmp/qiime2-q2cli-err-a8ngb9bw.log
I have also tried doing this command where I tried doing filter-samples using my table.qza after deblur (i previously already filtered things like Mitochondria and chloroplasts that I didn't want) with my simplified metadata file and then exported it, but it gave me a .biom file that I can't make any sense of (It opens with TextEditor but its mostly nonsensical):
You are very close, thanks for putting in the work to learn Qiime2! You need to take the output of your qiime feature-table filter-samples and put it into qiime feature-table filter-seqs
You will need to run the commands from filter-table filter-seqs
The commands should be:
Can you please provide your table where you filtered down to one sample ( should be your output from qiime qiime feature-table filter-sample and your output from qiime feature-table filter-seqs.
qiime feature-table filter-sample should filter down your table to one sample. qiime feature-table filter-seqs should filter your sequences down to just sequences in that sample.
This worked! Thank you for your help. Some of my confusion was that the filtered vs unfiltered repseqs files looked very similar, but when looking closer I noticed that it did indeed filter, but this particular sample just has many more sequences compared to the other samples!