Hi @mamunnoz,
You can use RESCRIPt's filter-seqs-length-by-taxon, or filter-seqs-length. Then you can run the following command to filter the table to keep the sequences output from one of these commands (i.e. the sequences-to-keep.qza
file):
qiime feature-table filter-features \
--i-table ./table.qza \
--m-metadata-file ./sequences-to-keep.qza \
--o-filtered-table ./table-keep.qza
-Mike