Features present in only one sample

[kla89]

Dear all,

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?

Best regards.

[Nicholas_Bokulich]

Hi @kla89,
Could you please provide some more information on your data? E.g.,

1. what type of library preparation and sequencing methods are you using? (in particular, what type of barcodes, primers, and marker gene are you using?)
2. what is the length of your sequences?
3. 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?

[kla89]

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.