miRge 2.0 for comprehensive analysis of microRNA sequencing data

BMC Bioinformatics

Table 2 Annotation comparison of the first version of miRge, miRge 2.0, miRDeep2 and miRAnalyzer

Tissue/Cell	SRA References	Alignment Tool	Processing time	miRNA Reads	Unique miRNAs	miRNAs > 10 RPM
Human Adipose Tissue	SRR772563	miRge - mb	35 s	2,041,433	484	240
		miRge 2.0 - mb	36 s	2,039,835	477	238
		miRge 2.0 - MDB	35 s	2,034,710	390	220
		miRDeep2	9.3 min	1,981,793	598	224
		miRAnalyzer	30 s	1,752,855	689	243
Human Alpha Cell	SRR1028924	miRge - mb	14.6 min	44,124,580	920	293
		miRge 2.0 - mb	15.6 min	43,880,855	911	279
		miRge 2.0 - MDB	15.0 min	43,752,598	583	261
		miRDeep2	56.0 min	42,326,135	864	267
		miRAnalyzer	18.4 min	34,349,816	1124	281
Human Beta Cell	SRR873410	miRge - mb	6.5 min	26,196,298	896	297
		miRge 2.0 - mb	6.6 min	26,197,845	889	291
		miRge 2.0 - MDB	6.5 min	26,130,904	585	274
		miRDeep2	34.1 min	23,280,604	754	273
		miRAnalyzer	8.0 min	14,240,669	1113	289
Mouse Stomach Tissue	SRR3653378	miRge - mb	2.0 min	7,063,128	804	457
		miRge 2.0 - mb	2.3 min	7,175,534	806	420
		miRge 2.0 - MDB	2.2 min	7,094,217	578	378
		miRDeep2	18.5 min	6,738,987	748	387
		miRAnalyzer	2.5 min	6,818,220	1086	423
Mouse Epididymal Epithelial Cell	SRR2075702	miRge - mb	3.0 min	1,394,193	435	364
		miRge 2.0 - mb	3.6 min	1,387,591	411	290
		miRge 2.0 - MDB	3.4 min	1,381,670	360	271
		miRDeep2	24.4 min	1,367,627	402	212
		miRAnalyzer	3.0 min	925,019	532	270
Mouse B3 Cell	SRR2960463	miRge - mb	3.7 min	9,515,760	604	322
		miRge 2.0 - mb	3.9 min	9,612,571	606	282
		miRge 2.0 - MDB	3.9 min	9,553,713	359	227
		miRDeep2	32.6 min	8,321,228	487	251
		miRAnalyzer	4.2 min	6,856,264	819	289

Key: mb = miRBase; MDB = MirGeneDB. Starting read counts: SRR772563 = 2,373,604 reads; SRR1028924 = 82,497,527 reads; SRR873410 = 33,233,648 reads; SRR3653378 = 9,587,887 reads; SRR2075702 = 13,890,643 reads; SRR2960463 = 17,652,076 reads

ISSN: 1471-2105