Does anybody know how to deal with data like this. What's worse, all of the data was generated around repeat elements. Alignment was good, but rmdup could reduce >50% data, and snp calling has a very high false positive rate.
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you should first tell us what kind of data you have??
NGS data for ChiP-seq, RNA-seq?
or
see this http://seqanswers.com/forums/showthr...cates+chip-seq
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Originally posted by harryzs View Postyou should first tell us what kind of data you have??
NGS data for ChiP-seq, RNA-seq?
or
see this http://seqanswers.com/forums/showthr...cates+chip-seq
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Originally posted by kopi-o View Post50% duplicates is not at all uncommon, it is impossible to tell whether it is worrying or not without details about how the data were generated.
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