2nd end of paired end starting with same sequence as first end!

[Benjamin Berman]

I am trying to interpret a paired-end 72bp GAII dataset. In a large
fraction of the reads, the sequence of end2 has a 5' end which is
identical to that of end1, but then diverges at some point 10 or more
bp into the read. A fraction of the end2 reads are alignable in the
correct orientation and distance from end1, but they tend to have
mismatches at the 5' end where they match end1 rather than the
reference sequence.

Has anyone heard of this or have any idea what could lead to this
seemingly strange phenomenon?

Thanks,
ben.

[Adam Ewing]

Hi Ben,

Are the sequences from end1 generally alignable without trimming? If so, could their protocol have involved any kind of self-ligation step (i.e. circularization)? I can maybe imagine a scenario where circularized products were inverse-primed with one of the primers offset ~10bp from the point of ligation, that might cause what you've described but I can't imagine why somebody would have done that.

-Adam

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