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Fig. 4 | BMC Genomics

Fig. 4

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

Fig. 4

Comparison of Subjunc, TopHat2 and TopHat2G among a total detected junction number and the number of junctions in RefSeq (known junctions), b junction detection. Over 130,000 junctions were detected by all the three methods, yet a large number of junctions were uniquely identified by individual method, c sequencing saturation in junction discovery. As sequencing depth increasing, Subjunc detected more novel junctions (total junctions minus junctions in RefSeq) than TopHat2 and TopHat2G, d efficiency of junction reads alignment. X axis is the read length; y axis is the proportion of junction reads in all mapped reads (junction reads number/total mapped reads number). TopHat2G is more efficient in aligning junction reads compared to Subjunc and TopHat2, especially for long reads

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