This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to demultiplex Unindexed.fastq.gz files?

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.

bcl2fastq illumina
• 4,400 views • link
updated by GenoMax GenoMax • written by a.rex a.rex

2 answers

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

• 1 views • link
written by GenoMax GenoMax

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.

• 1 views • link
written by h.mon h.mon

Log in to answer this question.

More posts like this