Hi all,

I was recently given a data set (run through Illumina in 2014) to merge with a set run through Illumina this year. The set I just received was not demultiplexed and was dual barcoded. I know that Illumina's bcl2fastq can handle dual barcoded sets and demultiplex, but I don't have any of the BaseCall data it typically uses to demultiplex. I only have .fastq.gz files and a mapping file to work with. Does anyone know if I can still use the bcl2fastq without the BaseCall data, or if there is something that would work better?

tldr; I need to demultiplex dual barcoded .fastq.gz files
You can't use bcl2fastq for this.

The bad news is that there might not be a tool to do as it is a task that is usually handled at the instrument level so there is less of a need to do it.

You would probably need to use a tool designed for cutting adapters to filter the reads:

http://cutadapt.readthedocs.io/en/stable/guide.html#filtering-reads

if it is a single end sequencing then this might be sufficient. If the reads are paired-end you'd probably need to process/reconcile both pairs to keep them in sync.

