Quality Score Binning on HiSeq 2500

[sklages]

Hi,

somebody using "qscore binning" for v4 runs on HiSeq 2500?
Do you see any effects in downstream analysis (e.g. mapping and denovo assembly)?

It would make some things a bit faster and would save a bit of disc space (fastq, BAM).

What is your experience?

[GenoMax]

Brian had looked at Q-scores for HiSeq3000 data recently which are also binned (I think all new illumina sequencers from NextSeq on have binned scores, either by default or don't have the option to not have binned scores): http://seqanswers.com/forums/showpos...3&postcount=16

[sklages]

Thanks.
Yes, the "quality inflation" may be considered problematic. That's something I have no bearing on.

I'd be interested in hearing from people using v4 chemistry on HiSeq with qscore binning and if there are issues with that in downstream analyses..

I do see advantages with qscore binning but I am not sure if there are some (real world) disadvantages I have not encountered/considered.