Entering edit mode
23 months ago
Hey all,
I have sequenced some short, dual-index libraries in paired-end mode using a two-channel NextSeq Illumina sequencer.
As expected, because the DNA sequences (inserts) are short, I end up sequencing the Illumina adaptors themselves (similarly to what happens when you sequence e.g. microRNAs). In the Read 1 fastq files, when I search for the Truseq P7 sequence (obtained here) I see that following each read are 6 A nucleotides followed by many G's, e.g.:
From other sources (e.g. here and here) I know that the G's result from no signal in two-channel sequencers such as the NextSeq 2000. I haven't been able to find an answer for what causes the 6 A's that appear after the P7 sequence and before the Poly-G sequence. Can anyone explain this?
That may be part of the anchors on the flowcell surface. AFAIK there are some parts of the flowcell chemistry that are trade secrets with no public information available.