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Old 02-12-2012, 07:38 PM   #21
Arjan
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also, i'm pretty sure the data i'm looking at is real and that the bias is a preference for certain fragments over others. i think chopping them off may not change my results for the good. i am however interested in an explanation for this bias.
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Old 02-20-2012, 04:08 AM   #22
pmiguel
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Quote:
Originally Posted by Arjan View Post
also, i'm pretty sure the data i'm looking at is real and that the bias is a preference for certain fragments over others. i think chopping them off may not change my results for the good. i am however interested in an explanation for this bias.
I could speculate... How about: the DNA has nicks at those sites? Then sonication might preferentially snap the chromatin strands there. Or, those sequences are preferred by T4 DNA ligase and get adapter ligated at a higher efficiency than others ends.

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Old 02-21-2012, 10:54 AM   #23
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hmm. okay. i have been trying to find literature on this but to no success so far. thanks.
You might try looking at http://www.ncbi.nlm.nih.gov/pubmed/20395217
The appropriate panel of figure 1 is nearly the same bias pattern as what you are showing.
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Old 03-09-2012, 01:52 PM   #24
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How are you fragmenting your chromatin? There is usually a bias in the first few bases if you are digesting your chromatin with micrococcal nuclease (Mnase). Here is a link to a paper that talks about this:

http://www.sciencedirect.com/science...22283608014824
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