Normalisation of Data

before rarefying I have this:

After raryfing:

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 \

--i-table rarefyall.qza
--o-visualization rarefyall.qzv
--m-sample-metadata-file metadata.tsv

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?

Hi @TurboQiimer,

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.


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Thanks @jwdebelius,
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

Hi @TurboQiimer,

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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