Transcriptome assembly and quantification from Ion Torrent RNA-Seq data

BMC Genomics

Table 2 Sensitivity and PPV comparison between methods for different combinations of read and fragment lengths: (50 bp, 250 bp), (100 bp, 250 bp), (100 bp, 500 bp), (200 bp, 250 bp), (400 bp, 450 bp).

Read	Fragment length	Methods	# assembled transcripts	# confirmed annotated transcripts	Sensitivity (%)	PPV (%)
50	250	Cufflinks	18,483	14,179	67.36	76.71
		MaLTA	20,036	15,894	75.53	79.33
		IsoLasso	19,422	15,287	70.66	78.71
100	250	Cufflinks	17,981	14,073	69.30	78.27
		MaLTA	19,405	15,539	76.72	80.08
		IsoLasso	16,864	12,802	62.60	75.91
	500	Cufflinks	18,958	14,757	67.19	77.84
		MaLTA	20,481	16,326	74.73	79.71
		IsoLasso	17,979	13,428	60.29	74.69
200	250	Cufflinks	20,435	15,637	66.57	76.52
		MaLTA	21,823	17,265	74.89	79.11
		IsoLasso	19,422	15,287	70.66	78.71
400	450	Cufflinks	18,483	14,179	67.36	76.71
		MaLTA	20,036	15,894	75.53	79.33
		IsoLasso	19,422	15,287	70.66	78.71

ISSN: 1471-2164