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 to demux standalone fastq.gz files. You can take a look at this thread (https://www.biostars.org/p/270737/ ) to get inspiration on how to do the demultiplexing of your dataset.

Edit: If you have in-line index sequences then a different solution would be needed. If you have standard Illumina datafiles (post what you get from @h.mon's command) then `demuxbyname.sh` from BBMap will work as indicated in the thread in my answer above and the original solution referenced there.