Due to technical issues while sequencing our DNA, the machine was stopped (bad quality scores). However we have many reads without barcodes. We want to align these sequences to the database to see what the taxonomy is. I have to created rep-seqs.qzv and table.qzv with a sample-metadata.tsv (articificial). However, the problem is that the sequences do not have any barcodes… so I don’t get any results in my two files. How do I go from here? (Note. I also imported the reads with manifest.csv.)
That’s unfortunate! If your quality scores are bad, you’ll have to avoid any of the quality-filtering steps that utilize quality scores, including denoising your data I’m not sure that you’d be able to perform any reliable analyses on these data (e.g. that could be published), but if your goal is simply to get a quick look at the data to see what taxa are there, see below.
Are you wanting to perform OTU picking against a reference database (e.g. closed-reference or open-reference OTU picking), or are you just wanting to perform taxonomy classification on your raw sequences to get a sense of the taxa that are present?
If it’s the latter case, probably the easiest way to go is avoiding QIIME 2 altogether. You could trying BLASTing the sequences (or a subset of the sequences) against NCBI’s Microbial Nucleotide database, which doesn’t require the installation of additional software if you use the NCBI website.
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