Strand In Pair-End Sequencing

Question

[Frenkiboy]

Is the Illumina pair end protocol inherently stranded?

That is, is it possible to define the strand the fragment came from just from pair end reads? (based on the strand of the first read in the pair)

Tnx!

Answer 1

[Arun]

No, Illumina protocols are not yet stranded. Normally, people deviate from the protocol to obtain strandedness. I remember the protocol a colleague of mine used being dUTP method. This paper explains it very nicely, especially the supplementary material (doc file) provides a nice idea of the working of SS method. There is also this paper which takes the same protocol but results in lesser cost by modifying certain reagents.