Sort of related to this…I’m wondering if there is a way to produce a separate barcode.fastq file when variable length barcodes are being used (In my case)?? I understand using extract_barcodes.py in qiime 1 (I’m quite familiar with many of the Qiime1 functions), but not sure if it’ll work in my case…
Hi @Thomas_Reid — unfortunately we don’t support this at the moment. We have created an issue to track development of this feature. Please see this forum thread for some discussion, as well.
Thanks!
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Just for reference, we have another open issue to add support for importing this type of multiplexed sequence data, where the barcodes are contained within the sequences. We’ll follow up here when it’s available in a QIIME 2 release!
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QIIME 2 2017.12 has a new cutadapt plugin which provides demux-single and demux-paired for demultiplexing reads where the barcodes are included within your reads!