" If either the full ApeKI site (from partial digestion or "chimera formation") or the first 8 bases of common adapter (from ApeKI fragments less than 64 bases) were detected within 64 bases, the read was truncated appropriately and then filled to 64 bases with polyA"
Could you put this into a wider context (e.g. explaining the rest of the protocol or with a reference to the article) ?
Still, it looks like a GBS protocol. If so, chimera in this case means that you have some chances that when you are ligating your adaptors for the PCR step (and then the sequencing), you may ligate another DNA fragment with the ApeKI site rather that the adaptors. Initially it is favored the ligation of the adaptors because the concentration is much higher, but you still have some chances to ligate other fragment of DNA from your sample.
- Badges
- Science method