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[…] n for studying regulatory mechanisms during human early embryogenesis. In fact, recent studies on human early embryogenesis have revealed that many important biological events, such as gene expression, X chromosome inactivation (XCI), and embryonic left-right separation, occur in a stage-specific fashion. We demonstrated that RNA editing could describe the genetic relationship between species through the evolution analysis of RNA editing in Drosophila species and the primate lineage. The consistent evolutionary pattern of RNA editing found in Drosophila species and the primate lineage agrees well with findings from previous studies,. These results demonstrated the broad applicability of our DeepRed method and confirmed the reliability of DeepRed from an application point of view., Taken together, our DeepRed method could decipher the hidden principles behind RNA editing by extracting and learning features from the raw sequences directly and predicted RNA editing sites accurately without prior-knowledge-based filtering steps or genome annotations. Our DeepRed method will make the detection of RNA editing convenient and effective and will facilitate the study of RNA editing., Considering that no gold standard set of RNA editing sites has been experimentally verified across various cell/tissue types, we constructed a positive set (RNA editing sites) and negative set (SNPs and other SNVs) using 64 RNA-seq samples of 32 cells/tissues (two replicates per cell line) from the ENCODE project. For each cell type, we used STAR (Version: 2.5.2b) and GATK (version 3.5.0) to call SNVs from RNA-seq data, then used the separate samples or pooled samples method proposed by Li’s group to identify the RNA editing sites (see “Supplemental materials”). Thus, the candidate SNVs were classified into RNA editing sites, SNPs and other. Then, we constructed separate and pooled gold standard sets for each cell using the RNA editing sites identified by the separate samples and pooled samples methods as the positive set and using SNPs and other SNVs as the negative set (Table ). The ratio of A-to-I editing sites in the positive and negative sets are 86.3% and 34.8%, respectively (Fig. ). Of the 32 cells/tissues, we carefully selected 11 cells/tissues an […]

Pipeline specifications

Software tools DeepRed, STAR, GATK