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Table 1 Results on other datasets

From: mmquant: how to count multi-mapping reads?

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
  1. 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