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Old 12-30-2009, 11:02 AM   #11
abelhj
Junior Member
 
Location: SLC

Join Date: Dec 2009
Posts: 4
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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.

Thanks,
hja
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