I am a little confused about the SE sequencing:
When the double strand fragment has been added adapters, it will be split into 2 single strands, after they go into the lane, I thought both will bind to the adapters on the lane surface, maybe distant from each other. Then they will form their own clusters and be sequenced, question comes, is this kind of sequencing of both the reverse-complement single strands the same as PE sequencing? Or do I misunderstand something in between?
Hope someone could clarify this for me! Thanks!
1 answer
Check the Illumina video at about 1:40min. During cluster generation both strands are present, but one strand is washed away prior to sequencing. In single-end mode, this remaining strand is sequenced. In paired-end, after the readout of the first strand is finished, this one is bridge-amplified again, but this time the forward strand is washed away, and the sequencing now happens for the reverse strand.
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