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What could have caused a matepair library to contain all pair-end reads.Shearing for a 3kb was done and analyzed on the agilent.
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The unbiotinylated fragments can carry over and be made into libraries. I have had to use the optional wash buffer (Streptavidin BWB 2) to remove more of these from the beads.
When looking at the data be sure to look at the difference between inward facing and outward facing paired reads. The inward facing are the regular PE-reads from the unbiotinylated fragments, the outwards are the mate pairs. -
I have been losing almost all of my samples after the Exonuclease treatment (after circularization). My theory is that my 3KB fragments are failing to circularize? What could have caused this?
I have successfully prepped mate pair libraries before, but this never has happened... Please, any input will be appreciated! Thanks!Comment
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