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The recent development of third generation sequencing (TGS) generates much longer reads than second generation sequencing (SGS) and thus provides a chance to solve problems that are difficult to study through SGS alone. However, higher raw read error rates are an intrinsic drawback in most TGS technologies. Here we present a computational method, LSC, to perform error correction of TGS long reads (LR) by SGS short reads (SR). Aiming to reduce the error rate in homopolymer runs in the main TGS platform, the PacBio® RS, LSC applies a homopolymer compression (HC) transformation strategy to increase the sensitivity of SR-LR alignment without scarifying alignment accuracy. We applied LSC to 100,000 PacBio long reads from human brain cerebellum RNA-seq data and 64 million single-end 75 bp reads from human brain RNA-seq data. The results show LSC can correct PacBio long reads to reduce the error rate by more than 3 folds. The improved accuracy greatly benefits many downstream analyses, such as directional gene isoform detection in RNA-seq study. Compared with another hybrid correction tool, LSC can achieve over double the sensitivity and similar specificity. 相似文献
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Analysis of cell movements and fate mapping during early embryogenesis in Drosophila melanogaster 总被引:5,自引:0,他引:5
Four spatially differentiated surface regions, called aeropyle crown, flat, stripe, and micropyle, are found on the mature eggshell (chorion). Specializations of the apical surfaces of the secretory follicular epithelial cells are implicated in the formation of regional patterns on the chorion. Some of these specializations are restricted to cells overlying certain regions; others are shared by more than one region. Differences between regions are more apparent on the surface than within the bulk of the chorion. Evidence is presented that distinct cell populations, corresponding to the regions, are present long before the start of choriogenesis. One hundred eighty-six chorion-specific polypeptides have been resolved by two-dimensional gel electrophoresis. Fifteen of these are found entirely or predominantly in the aeropyle crown and stripe regions, while eight others are restricted to the aeropyle crown region. Certain of the spatially restricted components are quite unusual in their amino acid compositions when compared with previously analyzed chorion components. Others are closely related, although clearly distinct. 相似文献
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