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Old 11-17-2011, 01:04 PM   #9
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Join Date: Jun 2010
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Originally Posted by HESmith View Post
There's an alternative approach, assuming that you have not yet constructed the libraries. Design them so the junction is at the opposite end of the insert, and perform paired-end sequencing. Cluster calling is based only on the first five cycles of read one, so you'll avoid the low-complexity issue.
Yep, exactly. Sadly my boss insisted on having a library that we can do single read OR paired end on (a money saving move potentially), so I had to design the junction on the first read side. And the samples are just about finished being prepped :/
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