A new strategy to reduce allelic bias in RNA-Seq readmapping
A new strategy to reduce allelic bias in RNA-Seq readmapping
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DOI：
10.1093/nar/gks425
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发表时间：
2012-09-01
影响因子：
14.9
通讯作者：
Reifman, Jaques
中科院分区：
文献类型：
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作者：
Satya, Ravi Vijaya;Zavaljevski, Nela;Reifman, Jaques
从RNA-seq数据中对表达水平的准确估计需要序列的精确映射读取为参考基因组。由于标准参考基因组在任何给定的基因座上仅包含一个等位基因，因此携带非参考等位基因的重叠多态性位点至少与参考文献不匹配，因此映射的可能性较小。读取映射的偏见导致等位基因特异性表达（ASE）的估计不准确。为了解决这种读取映射偏差，我们提出了一个增强的参考基因组的构建，该基因组包括已知多态性基因座的替代等位基因。我们表明，映射到此增强的参考文献减少了读取映射偏差，从而导致对ASE的更可靠的估计。模拟数据上的实验表明，与先前依赖于掩盖多态性基因座的方法相比，提出的策略将映射偏差的基因座数量减少了63％，而与使用未更换的参考参考的标准方法相比。当我们将策略应用于实际的RNA-seq数据时，我们发现它比以前的方法绘制的读取多达15％，并确定了许多看似不正确的推论。
Accurate estimation of expression levels from RNA-Seq data entails precise mapping of the sequence reads to a reference genome. Because the standard reference genome contains only one allele at any given locus, reads overlapping polymorphic loci that carry a non-reference allele are at least one mismatch away from the reference and, hence, are less likely to be mapped. This bias in read mapping leads to inaccurate estimates of allele-specific expression (ASE). To address this read-mapping bias, we propose the construction of an enhanced reference genome that includes the alternative alleles at known polymorphic loci. We show that mapping to this enhanced reference reduced the read-mapping biases, leading to more reliable estimates of ASE. Experiments on simulated data show that the proposed strategy reduced the number of loci with mapping bias by epsilon 63% when compared with a previous approach that relies on masking the polymorphic loci and by epsilon 18% when compared with the standard approach that uses an unaltered reference. When we applied our strategy to actual RNA-Seq data, we found that it mapped up to 15% more reads than the previous approaches and identified many seemingly incorrect inferences made by them.