Let me explain the question. As the image on the top, I have R1 and R2 fastq but no barcode.fastq, and I was told that the R1/R2 fastq does not contain any barcode sequence (removed). But I noticed that barcode info was in the fastq ID, and it's composed of 8mer+8mer. In each sample, the barcode tags in the fastq label are the same for R1 and R2.
Please teach me how to import this kind of data into qiime2, thank you very much!
Are these reads multiplexed, or demultiplexed (per sample)?
If they are already demultiplexed, no need to worry about the barcode in the label, you can just import as-is, using the fastq manifest format. If the reads are multiplexed, you are going to need to find a way to demultiplex them outside of QIIME 2, then import them using the fastq manifest. Let us know!
Hi Matthew, thanks for replying. I saw this post after I asked this question, and I follow the solution and it seems work, now running DADA2 (so my fastq probably are demultiplexed)
Just one last question, does multiplexed means barcodes are contained in the fastq sequences? If possible, I suggest to put the definition of "multiplex sequence" on the Qiime2 "core concept" page, thank you very much!
No not necessarily. It just means that the raw sequence file contains multiple samples — barcodes could be in the sequences, in a separate barcodes sequence file, in the header line, etc...
This is not a "core concept" of QIIME 2. Nor is this even unique to massively parallel sequencing. Many different biological techniques involve multiplexing (and probably non-biological too but I do not know). A very non-technical definition of (de)multiplexing is discussed in the overview tutorial. We have not sought to define this term (or indeed many others) because they are more general terms used in biology/molecular methods.
