Hi, @Nicholas_Bokulich,
Thanks for the detailed answers. Also again thanks to @Mehrbod_Estaki. May I know more details about the following? Thanks in advance.
(1) I am more understanding the suggestion one of q2-fragment-insertion. I am still trying now.
a. I have tried the code
qiime fragment-insertion sepp \
--i-representative-sequences rep-seqs-341.qza
--o-tree insertion-tree-341.qza
--o-placements insertion-placements-341.qza
These codes have been running for more than one hour, still have no results comes out. I just have 3 samples in the testing. May I know is there any settings that can use multiple threads as DADA2 procedure did? Thanks.
b. As the github protocol listed code.
qiime fragment-insertion sepp
--i-representative-sequences rep-seqs.qza
--o-tree insertion-tree.qza
--o-placements insertion-placements.qza
(Does the rep-seqs.qza in this procedure means the results of merged rep-seqs.qza from primer 1 and the rep-seqs.qza from primer 2? I am not sure about the understanding)
qiime fragment-insertion classify-otus-experimental
--i-representative-sequences rep-seqs.qza
--i-tree insertion-tree.qza
--i-reference-taxonomy taxonomy_gg99.qza
--o-classification taxonomy.qza
Then I will get the final taxonomy result as the final taxonomy.qza similar to the Moving picture tutorial produced.
(2) About the trimming the longer reads to the overlapped region, such as 515f-806r. May I know are there any code or protocol can be used in QIIME2 or others? Thanks.
(3)I use the following command to merge the table, "qiime taxa collapse --i-table table.qza --i-taxonomy taxonomy.qza --p-level 7 --o-collapsed-table table-I7.qza". I have tried, and indeed this will give the result table only at the species level, NOT at OTU level. And I think I will not continue try this procedure. BUT very informative for me. Thanks.