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Fig. 3 | BMC Genomics

Fig. 3

From: An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq

Fig. 3

Comparison of Cuffdiff based methods (Cuffdiff + Subjunc, Cuffdiff + Subread, Cuffdiff + TMAP, Cuffdiff + TopHat2, Cuffdiff + TopHat2G), RSEM and Sailfish among a robustness in gene expression quantification accuracy, in which all methods yielded consistent results with MAQC-I TaqMan, such that high Spearman correlation coefficients were observed in general, while Pearson correlation coefficients of RSEM and Sailfish were higher and more stable than Cuffdiff based methods, b the number of detected genes. Sailfish detected more gene than any other methods. c Good concordances were observed between relative expression measures from the MAQC-I TaqMan and Proton platforms, d consistency in gene detection. A large proportion of genes were commonly detected by Cuffdiff + TMAP, Cuffdiff + TopHat2G, RSEM and Sailfish, although Sailfish detected more unique genes than the others

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