Hi all. I'm trying to do ChIP-Seq in two different fragmentation ways including sonication and MNase treatment, respectively. I'm wondering is it necessary to perform paired-end sequencing for ChIP-Seq? Although paired-end sequencing can help to distinguish the PCR duplicates from the duplicates in the original unamplified DNA, the possibility to observe the duplicates in the original DNA sample should be low with sonication. Right? I'm not sure about MNase treatment.
Thanks very much! Any reply will be greatly appreciated.
Best
Thanks very much! Any reply will be greatly appreciated.
Best
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