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Old 08-28-2015, 01:38 AM   #1
Junior Member
Location: China

Join Date: Jul 2010
Posts: 7
Default masked or unmasked genome reference for RNAseq

Hi guys. I aligned RNAseq data to unmasked genome and hard masked genome, respectively. The mapping rate of the the former was about 92% and the latter rate was about 75%. It seemed that about 20% RNAseq data aligned to the repeating sequences of genome. So, which genome reference was better for RNAseq data, the unmasked genome or the hard masked?
Thanks a lot!
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