Wheter adapter and other technical sequences can occur in any location within reads ?

Question

[demolidd77]

HI,

there is a sentence "Although adapter and other technical sequences can potentially occur in any location within reads" in the trimmomatic manual ,

as I know , adapter sequences(adapter reverse complementary sequences) should only occur in the 3'end of every read , so why this manual says like it occurs in any location ....

could you please give me a detailed explaination ？

much thanks !

Answer 1

[Jean-Karim Heriche]

All technologies can produce artifacts. In this case, a possible origin could be that the reaction used to attach adapters to the DNA fragments of interest can not be perfectly controlled. For example, depending on the technology used for library preparation, it may be possible for DNA fragments to be attached at both ends of an adapter.