一种针对RNA-Seq 数据的基因异构体表达水平计算方法

doi:10-3969/j.issn.0258.8021. 2013.04.011

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Abstract RNA-Seq is a new experimental technique for trancriptome research based on highthroughput sequencing. It is increasingly used in the research of alternative splicing variation. There are two difficulties in the analysis of RNA-Seq data. One is readisoform multimapping, the other is nonuniform distribution of reads along the gene reference sequence. This paper proposed a new method, so called LDAseq, to calculate isoform expression level based on LDA (Latent Dirichlet Allocation) commonly used to model text corpora. LDAseq utilized the known geneisoform annotation to constrain the hyperparameters for dealing with readisoform multimapping. To modeling the non-uniform distribution of reads along reference sequence, LDAseq introduced “probes” with fixed length to break up the long reference sequence. We applied LDAseq to a mouse dataset and a human breast cancer dataset, and compared the performance of LDAseq with currently used alternatives, such as Cufflinks and RSEM. Results showed that the computation accuracy of LDAseq was increased 75.5% and 62.8% compared with that of Cufflinks and RSEM, respectively.

Key words： RNA-Seq isoform expression multi-mapping LDA probabilistic model

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	LIU Xue Jun^* LI Meng ZHANG Li

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LIU Xue Jun^* LI Meng ZHANG Li. A Method of Isoform Expression Calculation for RNA-Seq Data[J]. journal1, 2013, 32(4): 454-463.

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http://cjbme.csbme.org/EN/10-3969/j.issn.0258.8021. 2013.04.011 OR http://cjbme.csbme.org/EN/Y2013/V32/I4/454

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