Qiime filter feature table by sequences

Technical Support
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1

Hi, I am finding a difficulties in filtering. Here, we can filter feature table and sequences. We can also filter sequences by feature table by using qiime feature-table filter-seqs .

But if we first filter sequences like this way,

qiime quality-control exclude-seqs \
    --i-query-sequences ./rep_set-no-ecmu.qza \
    --i-reference-sequences ./references/silva-138-99-seqs-515-806.qza \
    --p-method blast \
    --p-perc-identity 0.90 \
    --p-perc-query-aligned 0.90 \
    --o-sequence-hits ./hits.qza \
    --o-sequence-misses ./misses.qza

How can we filter the feature table according to the above filtered sequences?

TIA

2

HI @Md_Shaminur_Rahman, you can simply run:

qiime feature-table filter-features \
    --i-table ./table.qza \
    --m-metadata-file ./hits.qza \
    --o-filtered-table ./table-hits.qza

More can be found here.

1 Like
3

Thank you so much, @SoilRotifer.

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