Double adapter1 meaning

[MaestSi]

Ask away!

Dear developers,
we are currently setting up a single-cell ONT protocol based on 5' capturing with 10x Genomics kit and target gene amplification. According to the documentation for 5' kit, adapter1 corresponds to Read1, while adapter2 corresponds to Non-Poly(dT) RT primer. Since our target amplification is based on a pair of primers that anneal on Read1 and on the target transcript, we expect that our target reads should carry only the Read1 adapter. Accordingly, I ran the pipeline with --full_length_only false parameter.
However, according to the pipeline report, most of our reads (> 80%) are "double adapter1". What does this specifically mean? Does this mean that most of our reads have Read1 adapter at both ends? If this is the case, we do not have a plausible explanation for their generation. Any suggestions?
Thanks in advance,
Simone

[nrhorner]

Hi @MaestSi

Yes, double_adapter1 means Read1 adapters were located on both sides of the read. This number is usually very low. I don't know what might be the cause of this.