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Old 12-10-2014, 11:41 AM   #1
Ingeneious
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Default Where does the read start?

The read starts reading the index, then the target specific primers and then the insert itself, correct?

So for example, I am using a 100 cycle kit, my index is 8bp long and I am doing 50bp PE reads, how much of my target insert would actually be sequenced? 92bp?
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Old 12-10-2014, 11:47 AM   #2
blancha
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The index has a distinct primer, and is sequenced separately.
50 bases will be sequenced from both ends of your insert.
I think there is a total of 108 cycles, to sequence the index in addition to the insert.
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Old 12-10-2014, 11:47 AM   #3
microgirl123
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Nope. You will sequence 100 bp of your insert (50 in each direction). The index is primed, sequenced, and read separately.
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Old 12-10-2014, 12:13 PM   #4
Ingeneious
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Great, thanks.
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