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Old 10-05-2011, 04:56 AM   #3
sehrrot
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Location: USA

Join Date: Jul 2010
Posts: 58
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I agree with pmiguel. that's very common in Truseq libraries. I don't know the reason but I've tried denaturing and it helps a bit. Also, I've considered if I put too much input for bioA but it's also observed in gel. So, last time I ran the gel and ut both 'larger peak' and 'normal peak', then sequenced. Both are basically same. I think it just conformationally bound to each other than increasing their size. I would say two peaks issue is fine but you would be bothered in measuring the mean size of your library, which is needed for your library QC and cluster density.

Apart from this issue, I wouldn't say that this issue is bird-nesting, I know this might be very arbitrary, but bird-nesting describes the situation that un-proper ligation makes two population within one sample - one is ligated (so shown in larger size) and the other is un- or partially-ligated (so shown in the size same as sheared DNA).
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