How to turn off Quality score binning in bcl2fastq

Question

[cmo]

Newer versions of bcl2fastq automatically bin the quality scores into just a few values. For example, for much of the recently-produced data I have worked with, all of the quality scores are one of: Q2, Q11, Q25, or Q37.

The command line help for bcl2fastq does not list any option to disable the binning of quality scores.

Is there any way to disable the binning of quality scores by bcl2fastq?

[Ahill]

Are you sure the Q-score binning is not happening upstream of the fastqs in the BCL level data, driven by the Illumina instrument software settings? Others here probably know much more, but a few links seem to suggest binning might be controlled there, and not in bcl2fastq.

Answer 1

[finswimmer]

As Ahill guessed, binning is done by the RTA during sequencing. The binning you are showing is done by RTA v3 used on NoveSeq. This step was essential to reduce output file sizes.

See here: https://www.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/novaseq-hiseq-q30-app-note-770-2017-010.pdf