Watson and Crick strand in Illumina sequence by synthesis

Question

[hakuna081017]

Not strictly saying, there are watson(5' to 3') and crick(3' to 5') strands in, for example, human genome.

Let's say we are sequencing the human genome by illumina pair-end method.

Are both of the watson and crick strand sequenced? Or one of the strand is discarded during the library prep?

According the video posted by illumina, in the 'sample prep' stage, the 3' end of the strands are tagged with the same binding complementary to the flow cell. But in the 'cluster generation' stage, only one strand shown. I just wonder does this stage applies to both watson and crick strands? If yes, how are these two strands reflected in the result, let's say fastq file?

I'm really confused by this and I've been searching for answers everywhere?

Hope I've presented my question clearly.

Thank you guys.

Answer 1

[GenoMax]

Actual sequencing is always 5' --> 3', and reported as such, so keep that in mind. Both strands have a chance of being sequenced equally since fragments can be made into libraries in either orientation (unless one of the strand specific library kits is being used for transcriptome sequencing).