before rarefying I have this:
It removed the higher frequencies and made them all at the same value. Is it normal? I am dubious about it! I think sth went wrong.
By the way, I run the related command without --m-sample-metadata-file metadata.tsv flag because first time I obtained this error:
qiime feature-table summarize \
Plugin error from feature-table:
The following IDs are not present in the metadata: 'Control week1', 'Control week2', 'Control week4', 'Control week6', 'NaCl-treated week1', 'NaCl-treated week2', 'NaCl-treated week4', 'NaCl-treated week6', 'SeaSalt-treated week1', 'SeaSalt-treated week2', 'SeaSalt-treated week4', 'SeaSalt-treated week6'
Would it be the case? If so, what is your suggestion to solve this?
The goal of rarefaction is to subsample to an even sequencing depth. So, the fact that you have the same sequencing depth (in this case, 79000 sequences/sample which was probably your rarefaction depth) is exactly what you should expect.
I confused. You mean the result I got is ok? The depth value has been chosen in my case is the lowest value you see.
Please notice this part I edited later. thanks alot
Yes, the result you go was okay.
The error message seems relatively self explanatory: “The following IDs are not present in the metadata”. If this is the case here, it may be an ongoing issue, so I would check your metadata throughly before proceeding.
the metadata issue was fixed. I got the same result. I think it is OK.
Please refrain from editing in these kinds of questions after the fact — it makes it difficult for us to address your original question, since hijacking like this turns the topic into a moving target (in my opinion). Next time, just open a new topic, or if you think it is relevant, post as a reply in the original topic. We get notifications when new posts and topics are created, but not when edits to random topics happen. This doesn’t mean don’t edit your post — if you see a typo, a mistake, or something that you think can be clarified, by all means, edit away. Its when you start layering on new questions that makes it difficult for us. Thanks for your understanding.
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