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Old 10-25-2011, 02:46 PM   #2
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Location: San Diego

Join Date: May 2008
Posts: 912

I guess you are running your own custom barcodes somehow? Like they are embedded in the sequence at both ends?

But in theory, if the reads came from the same flowcell, and lane, and tile, and xy-coordinates, (which is all in the original name given by Illumina to the read)they should be the two ends of the same DNA fragment.
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