Question: How 2-channel sequencing chemistry (Next-Seq) distinguish "G" and 'no signal'
gravatar for CY
22 months ago by
United States
CY460 wrote:

We found some samples enriched with "G" and we think this may caused by 2-channel sequencing chemistry can't distinguishing "G" and 'no signal'.

However, we have not have chance to sequence lot of sample using Next-Seq. Is 'no signal' or 'N' never appears in Next-Seq output? This seems to be a really serious flaw to me. Does it make sense?

qc next-seq • 681 views
ADD COMMENTlink modified 22 months ago by Devon Ryan93k • written 22 months ago by CY460

See for more on this issue.

ADD REPLYlink written 22 months ago by genomax76k
gravatar for Devon Ryan
22 months ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

You will commonly see an enrichment of GGGGGGGG sequences on a NextSeq for the reason you mentioned. As an example, when you demultiplex a run you will typically find GGGGGGGG to be the "unplaced barcode" with the highest count. This is, of course, actually NNNN. Yes, this is a known limitation of NextSeq machines. For that reason I wouldn't use them for things like BS-seq, where an individual G can have a lot of meaning.

ADD COMMENTlink written 22 months ago by Devon Ryan93k
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