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
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
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