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Old 06-23-2011, 06:58 AM   #4
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Location: Munich

Join Date: Jan 2009
Posts: 138

what is your model organism and how many mapped reads do you get? what's the mappability fraction of your reads?

i would also try to keep the duplicates as in my opinion the duplicate removal can potentially generate a HUGE problem if your IP works very well, there are very few target sites and you have tons of mapped reads. then you will elminate all your signals due to true, i.e. non-artificial, read duplication.

and do the qPCR on your library!

Last edited by mudshark; 06-24-2011 at 04:26 AM.
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