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Old 08-21-2013, 07:49 AM   #2
mcnelson.phd
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Location: Connecticut

Join Date: Jul 2011
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Because the Covaris uses acoustics to mechanically shear the DNA, you technically shouldn't see any bias like you might see if you were doing an enzymatic or transposon (Nextera) type fragmentation.

By size selecting well about where most of your fragments would be, you could have issues with really poor yields though, to the point that you'd have to either do more rounds of PCR or have to just remake the libraries again.

Even on a MiSeq, there's no harm by sequencing small fragments where read 1 and read 2 completely overlap. In fact, this happens quite often with Nextera sample prep, so you just have to be aware of sequencing into the adapter on the other end of the fragment and making sure you trim that off before you try doing your assembly.
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