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Old 12-30-2009, 11:20 AM   #1
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Default paired-end question


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.

GCCCxxxxxxATTT # ==> GCCC

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

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)?)

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Old 12-30-2009, 01:01 PM   #2
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For future reference, if you use the [ code ] .... [ /code ] tags it will use a fixed width font and be easier to align!
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orientation, paired-end, solexa

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