I'm having issues getting an OTU table that I can use to BLAST against different databases. I don't want to use the I have demultiplexed single-end sequences that I denoised in DADA2:
qiime dada2 denoise-single
Then I filtered sequences with less than 10 reads and that fell in less than 2 samples:
qiime feature-table filter-features
and qiime feature-table filter-features
and filtered sequences by the newest feature-table:
qiime feature-table filter-seqs
Now I have clustered sequences at 99% similarity:
qiime vsearch cluster-features-de-novo
I want to get a table that tells me sample ID, frequency of OTU per sample, and gives me the barcodes of OTUs so I can BLAST them. I also want to add my metadata table, but not sure during which step. Is something like that possible?
Hi @lnovak4 ,
The q2-feature-classifier plugin has a taxonomic classification method that is based on blastn, so you can just use your sequences as input to that method to achieve the first part of what you want (i.e., instead of using BLAST manually). The benefit of this method is that it automatically finds a consensus taxonomy (much better than taking the top blast hit or manually finding the consensus).
qiime metadata tabulate with the feature table, sequences, and taxonomy as inputs — see here for an example:
technically QIIME 2 can be used for this as well (also with
metadata tabulate), but this is beginning to sound like a customized table that you should probably prepare outside of QIIME 2, e.g., to export these files and merge/modify per your specifications. QIIME 2 cannot add metadata to both the sample and feature axes simultaneously, so creating such a custom report will require some custom work.
The issue I have is that I don't want to use BLAST for taxonomy, I have another database I want to use. Is there a way to get the clustered sequence barcodes in a table?
QIIME 2 can accept any database as input, provided that it is supplied in the correct format (see the online tutorials for formatting and importing details)
Sure, see the exporting tutorial:
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.