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

BMC Genomics

Table 1 Sequencing platforms, library preparation, and sequencing results

Sequencer	Fragmentation methods	Initial RNA(μg)	Library name	Library insert size(bp)	Mean read length(bp)	Raw Q10	Raw Q20	Raw Q30	Total reads	Total base
Ion Proton	Chemical	2	ProC_1	196	153	98.69 %	70.85 %	1.55 %	19,448,438	2,975,809,154
		2	ProC_2	179	138	98.70 %	69.81 %	1.34 %	25,262,605	3,505,548,278
		2	ProC_3	200	155	98.82 %	72.14 %	1.80 %	8,139,486	1,263,964,775
		2	ProC_4	166	136	98.80 %	72.31 %	1.79 %	23,866,259	3,267,082,715
		2	ProC_5	196	155	98.82 %	73.90 %	1.88 %	15,461,415	2,408,389,343
		0.2	ProC_6	175	137	98.74 %	69.79 %	1.35 %	22,673,571	3,123,633,358
		0.2	ProC_7	215	158	98.75 %	70.67 %	1.43 %	13,098,194	2,076,154,568
		0.2	ProC_8	180	140	98.82 %	71.57 %	1.61 %	23,142,854	3,251,986,105
		0.2	ProC_9	199	160	98.85 %	73.24 %	1.73 %	12,219,286	1,955,402,424
	RNaseIII	2	ProR_1	89	94	99.25 %	83.05 %	4.04 %	16,024,785	1,519,618,514
	RNaseIII	2	ProR_2	91	92	99.17 %	81.95 %	3.87 %	25,434,638	2,364,470,896
HiSeq 2000	Chemical	2	HiSeq_1	193	90;90	98.11 %; 95.11 %	97.03 %; 93.73 %	91.86 %; 88.43 %	60,313,246	10,856,384,280
HiSeq 2000	Chemical	2	HiSeq_2	187	90;90	97.72 %; 94.53 %	96.59 %; 93.06 %	91.51 %; 87.58 %	56,610,071	10,189,812,780

ISSN: 1471-2164