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[mRNA-seq] 计算机模拟测序数据来探索RNA-seq

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发表于 2016-11-25 16:39:38 | 显示全部楼层 |阅读模式
A limitation of using “real” data is that no ground truth exists, hence we next explored this more rigorously by performing a simulation study. We generated in silico data sets with different read lengths (50, 100, 150, 200 bp), overall coverage (10X, 30X, 60X, 120X) and with both single- and paired-end reads (see Materials and Methods for details). Note that each data set contains eight libraries. These data allowed us to assess how near the output of each pipeline was to the true expression values, the effect of sequencing depth on the results and whether longer reads lead to reduced errors. Obviously an ideal simulated data set should have properties similar to those observed in real data sets. However, to be able to compare all genes across different data sets thirty two data sets were generated in silico where all transcripts had approximately the same level of expression (referred as STE).

RNA-Seq Gene Profiling - A Systematic Empirical Comparison (PLoS One, 2014).
http://journals.plos.org/plosone ... ournal.pone.0107026



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