- forward reads fastq.gz (R1)
- reverse reads fastq.gz (R2)
- barcodes fastq.gz (R1.R3)
The barcodes should apply for the paired reads. But what if I’d just like to use the forward reads (R1)? Will the barcodes work with single end reads?
That depends on your barcodes set up. If they exist on both the forward and reverse primers, it is likely that the combination of the two are needed to demultiplex. So, you should demultiplex your reads first using paired-end reads then once they are demultiplexed you can simply discard your reverse reads to continue.
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