TABLE 1.

DESeq2 differential expression statistics^a

Quantification method	Cluster	No. of correct DE genes	No. of correct NDE genes	No. of missed DE genes	No. of false-positive DE genes	Detection rate (%)	False-positive rate (%)	No. of DE genes excluded from expression threshold	No. of NDE genes excluded from expression threshold
Salmon –validateMappings –allowDovetail	1	673	3,156	587	3	53.41	0.09	22	5
Salmon –validateMappings	1	674	3,156	586	3	53.49	0.09	22	5
Kallisto	1	673	3,150	587	9	53.41	0.28	58	4
eXpress -B10 –no-bias-correct	1	599	3,152	661	7	47.54	0.22	158	14
eXpress	1	290	3,119	970	40	23.02	1.27	163	17
featureCounts	2	694	3,154	566	5	55.08	0.16	97	15
FADU –remove-multimapped	2	703	3,156	557	3	55.79	0.09	92	15
HTSeq -m intersection-nonempty	2	656	3,156	604	3	52.06	0.09	156	17
HTSeq -m union	2	645	3,158	615	3	51.19	0.09	178	20
HTSeq -m intersection-strict	2	607	3,142	653	1	48.17	0.03	357	42
HTSeq -m union –nonunique all	3	770	3,142	490	17	61.11	0.54	51	6
featureCounts -O	3	776	3,142	484	17	61.59	0.54	55	6
featureCounts -O –fraction	3	735	3,146	525	13	58.33	0.41	52	6
FADU –em_iterations 10	4	686	3,149	574	10	54.44	0.32	52	10
FADU	4	684	3,152	576	7	54.29	0.22	53	9

^aDE, differentially expressed; NDE, nondifferentially expressed.