sidle tutorial missing aligned sequence file

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 "Database Preparation" or "Sequences Reconstruction" parts) inside the documentation that indicates how I can obtain the database/sidle-db-aligned-sequences.qza file. Could you, please, help me?

Thank you so much.

Regards,

Elsa

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 the "Sequence Reconstruction" Section) with the reconstructed-table and the database file without separating in regions?

Sorry for the missunderstanding!

Thank you!

Elsa

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 in the downloaded QIIME 2 folder. (Remember that tree building only works with greengenes 13_8 and Silva 128 right now. At somepoint we'll hopefully have more SEPP references, but this is where things are right now. :woman_shrugging:

Best,
Justine

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