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Old 04-19-2014, 09:54 AM   #20
Location: DC area

Join Date: Sep 2011
Posts: 42
Default Mapping uniquely

Hi I have a very basic question about read mapping. For differential expression analysis of NGS data , many papers I have read , mention that they discard non -unique mapping reads. However I could not find a good summarized explanation for doing so. From what I gather and understand, the more unique the read is the better certainty it is to call its location as the technique itself could introduce some mismatches and bring about non specific mapping and also the unique location depth would still account for the naturally exisiting SNPs if any.
Have I understood this right or is there a better explanation of why we take only unique mapping reads to perform differential expression?
THanks in advance
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