ScRNAbox: empowering single-cell RNA sequencing on high performance computing systems

BMC Bioinformatics

Table 1 Selected quality control measurements across all samples in the midbrain dataset

	Control						Parkinson’s Disease
Sample	1	2	3	4	5	6	1	2	3	4	5
Ambient RNA rate (%)	5.1	1.9	2.0	2.2	4.3	1.6	2.2	2.3	2.5	1.0	2.0
Minimum total RNA transcripts	501	500	506	500	501	501	500	504	503	501	501
1st quartile total RNA transcripts	2781	2913	2278	3375	2572	3351	2582	3092	2025	2668	3654
Minimum unique RNA transcripts	112	68	199	132	50	154	184	66	261	32	196
1st Quartile unique RNA transcripts	1478	1587	1346	1766	1490	1725	1448	1711	1276	2520	1896
Median % mitochondrial RNA	3.04	1.30	0.62	0.44	1.20	1.02	1.12	1.80	0.55	2.14	0.92
3rd Quartile % mitochondrial RNA	6.19	3.22	1.24	0.89	2.34	2.30	2.31	3.42	1.14	4.49	1.69
Median % ribosomal RNA	0.42	0.72	0.64	0.67	0.61	0.76	0.45	0.66	0.79	0.85	0.63
3rd Quartile % ribosomal RNA	0.65	1.16	0.88	1.00	0.87	1.22	0.73	1.14	1.25	1.31	1.13

ISSN: 1471-2105