Table 1.

Results on other datasets

Organism	D. melanogaster	M. musculus	A. thaliana	S. cerevisiae
GEO accession	GSE80323	GSE86865	GSE89850	GSE83827
reference	[16]	[17]	[18]	[19]
# exp. genes	16383	24516	25170	6722
# merged genes	7237	25302	5903	4782
type	paired	single	paired	single
# replicates	4	3	3	2
# reads	27M–33M	39M–47M	12M–16M	10M–14M
# hits	28M–34M	53M–70M	12M–15M	13M–17M
# fc genes	1446	13	4622	546
# htsc genes	1432	13	4557	546
# mm genes	1441	10	4599	388
# fc and htsc	1420	13	4503	546
# fc and mm	1415	10	4534	387
# htsc and mm	1399	10	4458	387
# mm merged only	191	2	394	97
fc time	1mn28–	1mn25–	0mn46–	0mn16–
	1mn56	2mn38	1mn10	0mn29
htsc time	36mn–	21mn–	20mn–	4mn11–
	46mn	25mn	26mn	5mn58
mm time	2mn35–	2mn06–	1mn19–	0mn20–
	3mn31	2mn42	1mn43	0mn28
mm time unsorted	3mn31–	2mn22–	1mn28–	0mn24–
	4mn18	2mn53	2mn11	0mn31

The description of each line follows. # exp. genes: number of expressed genes (at least one read in one of the replicates); # merged genes: number of merged genes found by mmquant; type: single-end or paired-end; # replicates: number of replicates in each of the two conditions; # reads: number of reads sequenced; # hits: number of hits given by STAR; # fc genes: number of differentially expressed genes found by featureCounts; # htsc genes: number of differentially expressed genes found by htseq-count; # mm genes: number of differentially expressed non-merged genes found my mmquant; # mm merged only: number of genes that constitute the differentially expressed merged genes, and that are not found by the other two methods; # fc and htsc: number of differentially expressed genes found by both featureCounts and htseq-count; fc time: time spent by featureCounts; mm time unsorted: time spent by mmquant, using unsorted data