How to demultiplex Unindexed.fastq.gz files?

Question

[a.rex]

I have downloaded the Unindexed.fastq.gz files from my Next-seq run using the python downloader.

How can I demultiplex these? Am I right in thinking that bcl2fastq requires bcl files? I do not understand why I cannot simply use the unindexed files that basespace generates?

If this is not possible, how can I download the bcl files from base space?

Thanks in advance.

Answer 1

[GenoMax]

If you know the sampleID_Index associations (and if the run actually included index cycles) then you can use one of the two threads below to get an idea of how to do the demultiplexing.

Demultiplexing Illumina data
Demultiplexing reads with index present in the labels

Answer 2

[h.mon]

You will need to provide more detail to get better answers, but...

If this Unindexed.fastq.gz is the result of a regular Illumina run, these are the reads that couldn't be assigned to any library, i.e., their barcode was not identified. Illumina barcodes are sequenced separately from the reads, and may be provided as a separate file, or "inline" within reads headers.