Nanopore incomplete fragment sequencing

Question

[VHahaut]

Hi!

I am analysing PCR products sequenced on a MinION from Oxford Nanopore. I observed that some of these reads do not contain both PCR primers, even though the read has been mapped from end to the other. It is like if the PCR product has been sequenced only partially (i.e., from one end to the middle of the fragment).

I know that some of these partial PCR products could come from the PCR itself but I was wondering if with Nanopore sequencing you could also get a fragment entering a pore, sequenced up to the middle of the fragment and then loose the rest of the fragment information.

Thank you in advance.