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Old 09-28-2017, 03:20 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
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In theory when the insert is shorter than the read length you do read into the adapter at other end and then will sequence the index. Problem is not all inserts in your library are the same length and may not even be shorter than read length. So you would not be guaranteed to reach and read the index each time. One would want the indexes to be read consistently so a separate primer is used to ensure that. Both Index 1 and 2 are read as separate reads.
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