Hi @lam and @jwdebelius , I am working with q2-sidle and right now some doubts has arisen for me. In the same step that @lam mentioned before: qiime sidle reconstruct-fragment-rep-seqs \ [...] --i-aligned-sequences database/sidle-db-aligned-sequences.qza [...] I could not find any place (in the…

Hi @elsamdea , I hope you're well! :wave: As I think is documented in the Sidle docs (and if not I will add it): tree reconstruction only works for databases that have SEPP reference trees. This means you can reconstruct using Silva 128 or Greengenes 13_8 if you want a tree. If you'd like to build …

Hi @elsamdea , The sidle-db-aligned-sequences.qza should be in the database folder you downloaded; please double check with ls. If it's not, then we can troubleshoot from there. The aligned sequence file is from the database and so it's something that gets provided during that step. Best, Justine

Hi @jwdebelius ! Perhaps I didn't explain myself correctly. I mean how I can build/obtain this file with my one database? In other words, not this file: sidle-db-aligned-sequences.qza particulary, but a file with contains my database aligned-sequences. Maybe should I re-do the alignment step (from…

Hi @elsamdea , As always, it depends on the database. If you're working with greengenes 13_8, there should be a directory called rep_set_aligned which will have a list of files showing a percent identity; pick the one that matches your identity (probably 99). If you're using Silva 128, I think it's …

Hi again! I think my question is also useful in this post, because it is related to another database. So that is the reason why I am posting this here and do not in a new post. I would love to reproduce the last step of sidle documentation's Phylogenetic Tree Reconstruction. However I could not fi…

Hi @jwdebelius ! I am good! How have you been? :slight_smile: [image] jwdebelius: As I think is documented in the Sidle docs (and if not I will add it): tree reconstruction only works for databases that have SEPP reference trees. I might be wrong, but I think I did not read that in the Sidl…

[image] jwdebelius: mepoint we'll hopefully have more SEPP referen Dear Elsa and Justine, I was confused by this last part of the tutorial. Would it be enough to align the sequences in the DB (Silva in my case) by myself in qiime? Where can I find the SEPP reference tree? Thanks in advance, …

Hi @nandreani , It sounds like I need to make it more clear in the documentation :slightly_smiling_face:. You need the aligned sequences for hte database; I think for Silva 128, they can be downloaded from the Silva website . The insertion scaffold is available from the resources page . Best, Justi…

thank you very much Justine! Nadia

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