@Jennifer_Fouquier Hi, I am new to qiime2 ITS analysis and was trying to use Fungal ITS analysis tutorial for analysing the fungal ITS using the UNITE database unite-ver7-99-seqs-01.12.2017. I could reach till taxonomic classification and would like to further analyse beta diversity using q2-ghost-tree. I have re-rooted the pre-built ghost-tree ghost_tree_80_qiime_ver7_99_01.12.2017/ghost_tree.nwk and got ghost-tree-midpoint-root.qza. Next, I have to filter my feature-table using
ghost_tree_80_qiime_ver7_99_01.12.2017/ghost_tree_extension_accession_ids.txt (If I understand the protocol correct). I looked for the
‘qiime feature-table filter-features’ arguments in https://docs.qiime2.org/2019.1/tutorials/filtering
but not able to understand what should be input parameters as we can only give one input for e.g our feature-table but how it will take reference from ghost_tree_extension_accession_ids.txt? I am bit confused at this point. Please guide me from ghost-tree filtering to beta diversity in qiime2.
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