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Old 05-25-2011, 03:53 AM   #2
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Location: Munich

Join Date: Jan 2009
Posts: 138

- did you confirm the SICER peaks by qPCR on unprocessed ChIP samples or any other technology?
- are there positive/negative regions already documented and do your sequencing results conform to those?
- my initial guess is that you a) do not have enough reads for a robust analysis b) differences in sequencing depth will be the main source for inconsistency. c) most of your SICER peaks are false positives
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