Hi, I've been trying to recreate a SeppReferenceTree steps from thread:
I’m new to qiime2, so I’m not sure if I’m having problems because I couldn’t find instructions for importing/creating a SeppReferenceDatabase.
Use a customized subset of Silva 138 NR99 for sepp fragment insertion.
What I’ve done:
Using arb, exported the aligned fasta for the high quality seqs I want to use, after trimming to just the relevant 16S region, and exported the corresponding tree.
Siavash’s steps to clean up the tree, resolve polytomies, and re-estimate branch …
Exports/taxonomy/tax_slv_ssu_138.1.tre.gz from last
SILVA release. Then I run
nw_topology -bI to prepare the tree.
I am intrested in creating
SeppReferenceDatabase for V4 region specifically.
For the moment I am particularly puzzled with masking step described
should I first filter reference sequences from SILVA to V4 region or do this masking step?
how should I choose the masking length properly?
should I take anything else into account to make the database reusable for community?
@dethlefs @hugh @Stefan your experience would be invaluable to accomplish this task.
@crusher083, welcome back to the forum!
Data Resources linked from the user docs are going to be your best bet within QIIME 2 - if those don't address your questions, I'd recommend posing your questions in GitHub - smirarab/sepp-refs. Hope this helps!
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.