I’ve imported paired end illumina sequences with the manifest method and run them through the dada pipeline. I end up with a feature table where each feature is only present in a single sample, which doesn’t make sense for these samples (and is very different from analysis with qiime1). Have you seen this before or do you have any ideas where I might be going wrong?
Could you please provide some more information on your data? E.g.,
- what type of library preparation and sequencing methods are you using? (in particular, what type of barcodes, primers, and marker gene are you using?)
- what is the length of your sequences?
- what is the command that you are using?
My guess is that you may have an in-line barcode or some other piece of non-biological sequence present within the sequence reads that is not being trimmed prior to dada2. This would cause each feature to be unique to a single sample. Does that make sense, based on your methods?
Thanks for getting back to me so quickly! You are right - the barcodes are still included these reads (from a different sequencing facility and I didn’t think to check). All sorted now, thanks again.
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