bcl2fastq output quality of index

[ezseq123]

Is there a way I can use bcl2fastq to output the quality score of the index (not just the quality sequence read).

[GenoMax]

Following is only valid for bcl2fastq (v. 1.8.4). May be possible to do something similar for v.2.x.x.

You can do it by running bcl2fastq (do you have access to an install and the full flowcell folder) with a clever use of "--use-bases-mask" option {Y*,Y*,Y* (if single end) or Y*,Y*,Y*,Y* (for paired-end)}.

You can't demultiplex the data in this mode since the tag reads are being treated as regular reads (provide a dummy sample name without any tags in the samplesheet).

You will get a R1,R2,R3 files for a single end run (R2 will be your tag read with Q-scores) or R1,R2,R3,R4 files for paired end runs (R2 and R3 will be your tag reads with Q-scores).

You would want to provide a separate --output-dir location for this special run.

[ezseq123]

Thanks GenoMax.
I suppose I will have to build my own demultiplexer for that.

[GenoMax]

You can run bcl2fastq 2 times. Once to get the demultiplexed output and other time to get the tag reads. Just specify two --output-dir locations for the two runs.

BTW: Why are you interested in Q-scores for tag reads?

[nucacidhunter]

Overall index Q scores can be viewed in Illumina SAV QScore Distribution plot. From the read tab, 2 will represent index 1 and read3 index 2 (for dual indexed runs).

[dpryan]

In the off-chance that you want to just use the most recent (2.something) version of bcl2fastq, you can just use the --create-fastq-for-index-reads option.