qiime feature-table filter-features question


I'm only interested in the 2019 samples in my metadata file, so I used qiime feature-table filter-features command.

The command worked well but I found that the number of the ASVs decreased a lot.

rarefied_table.qza this file contains 33616 ASVs and 699 samples
rarefied_table-2019.qza this file contains 16600 ASVs, and 211 samples. This is true that I only have 211 samples in 2019.

In my opinion, this command just filters the asv table based on --p-where '[Year]="2019"', why does the number of ASV reduce this much? Any help would be appreciated.

(qiime2-2023.5) busihan@SihandeMacBook-Pro core-metrics-results-nonphylo-renamed-unique-samples-genus % qiime feature-table filter-samples \
    --i-table rarefied_table.qza \
    --m-metadata-file 2024Mar14_Mapping_file_740.tsv \
    --p-where '[Year]="2019"' \
    --o-filtered-table rarefied_table-2019.qza
Saved FeatureTable[Frequency] to: rarefied_table-2019.qza

2024Mar14_Mapping_file_740.tsv (65.3 KB)
rarefied_table-2019.qza (713.6 KB)
rarefied_table.qza (1.6 MB)

Hi @Sihan_Bu,

It looks like you actually used qiime feature-table filter-samples is that correct?

It seems like you have a significant amount of features that are not found in your subset of only 2019 samples, Which would explain why that are missing in your new feature table.

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Yes, I used qiime feature-table filter-samples.

It makes sense. Thank you.

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@Sihan_Bu Glad I could help!

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