paired-end question

[abelhj]

Hi,

I am trying to figure out Solexa paired end read output. Can someone please tell me if my toy example is correct?

1) One end of DNA is bound to substrate (##). Free end is sequenced in 5'-->3' direction.


5'
------>
GCCCxxxxxxATTT # ==> GCCC
CGGGxxxxxxTAAA#




2) Opposite end of DNA bound to substrate (##). Free end of *complementary* strand sequenced in 5'-->3' direction.


5'
------>
AAATxxxxxxGGGC# ==> AAAT
TTTAxxxxxxCCCG #


So the final output of the Solexa machine would be the pair (GCCC, AAAT) and then a program such as maq would worry about the details of orientation/taking complements. (Or would the pair be (GCCC, TTTA)?)

Thanks,
hja

[ECO]

For future reference, if you use the [ code ] .... [ /code ] tags it will use a fixed width font and be easier to align!