I have seen duplicate percentage of 33% in targeted high coverage experiment and based on my assessment of false positive and false negative I am happy not removing duplicates.
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It depends on what your experiment is. In some cases it has very little effect, in some it can be detrimental. In no case that I've heard of does leaving PCR duplicates in your data improve your results, however.Originally posted by husamia View PostMendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
Projects: U87MG whole genome sequence [Website] [Paper]Comment
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Hi. everybody
I have a problem about remove duplicates,
In this study , http://www.ncbi.nlm.nih.gov/Traces/sra/?study=ERP000603
It's have 2 Experiments, and 13 RUNs,
How to do remove duplicates? by study? by Experiments? or by one runs?
Thanks !!Comment
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Remove PCR duplicates by library (and this looks like one big "library" mixed from 4 PCR pools). Optical duplicates are removed by lane (but I guess Picard would detect the within lane reads, given proper read group labelling).Comment
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