Influence of RNA extraction methods and library selection schemes on RNA-seq data

BMC Genomics

Table 1 Mapping statistics

Group	Sample	All reads	Mapped reads	Pairs	Mapped, MAPQ > 1	Mapped on exons (%)	Mapped on introns (%)	Mapped on introns (%) mapped to non annotated regions (%)	Mapped on rRNA (%)	Mapped on mitochondrial DNA (%)	Unique starting position (%)
PolyA Trizol	Tot_RNA1	101028616	93699257	78996022	83038355	86,7	10,7	2,6	0,31	4,80	32,4
PolyA Trizol	Tot_RNA2	103480788	96072826	81214720	84983881	86,7	10,7	2,6	0,31	4,80	32,4
PolyA Qiagen	Tot_RNA3	100766522	100766522	76780490	82231228	91,3	6,6	2,1	0,30	4,58	28,5
PolyA Qiagen	Tot_RNA4	109645220	109645220	83720316	89300384	91,3	6,6	2,1	0,30	4,58	28,5
RiboZ Trizol	Tot_RNA1	109221096	103587793	92825224	85242138	60,6	35,1	4,3	0,04	0,39	51,5
RiboZ Trizol	Tot_RNA2	113936740	107997806	96763362	90980604	60,6	35,1	4,3	0,04	0,39	51,5
RiboZ Qiagen	Tot_RNA3	118950948	118950948	110394536	91193892	81,6	15,6	2,8	0,02	0,28	35,1
RiboZ Qiagen	Tot_RNA4	112056778	112056778	88450950	86755352	81,6	15,6	2,8	0,02	0,28	35,1
RiboZ cytoplasmic	Cyt_RNA5	111517838	102989353	86770814	87248867	87,1	10,3	2,6	0,03	0,56	31,3
RiboZ cytoplasmic	Cyt_RNA6	102998772	94630661	79109400	87248867	87,1	10,3	2,6	0,03	0,56	31,3
RiboZ nuclear	Nuc_RNA7	126297526	122854406	116663678	115579529	31,1	60,8	8,2	0,01	0,05	65,2
RiboZ nuclear	Nuc_RNA8	127905406	124011269	117109650	116428981	31,1	60,8	8,2	0,01	0,05	65,2

The numbers of mapped sequence reads are given as absolute numbers. Percentages are calculated according to the total number of reliable reads (MAPQ > 1). The number of unique starting positions is a measure of the library complexity.

ISSN: 1471-2164