Table 1 Number of features (genes plus gene complexes), the number of genes covered by any of the features (# incl. genes), the number of counting bins, and the sum of all bin counts for various counting methods and for the complete and reduced annotation catalog. Randomly excluding 20 % of the transcripts from the annotation catalog generally led to a slight increase in the average bin count, with the most pronounced effects seen for the methods defining the counting bins as (combinations of) transcripts (kallisto and MISO). MISO and SplicingGraph consider only genes with at least two isoforms, which explains the lower number of features for these methods
| Â | Â | Fruit fly | Human | ||
|---|---|---|---|---|---|
| Â | Â | Complete | Incomplete | Complete | Incomplete |
casper | # features | 11,505 | 10,282 | 12,544 | 12,636 |
| Â | # incl. genes | 13,284 | 11,615 | 15,577 | 15,157 |
| Â | # bins | 555,346 | 491,188 | 3,523,252 | 3,076,596 |
| Â | Tot count | 18,583,949 | 16,621,279 | 38,024,617 | 35,159,482 |
| Â | Tot count/# bins | 33.46 | 33.84 | 10.79 | 11.43 |
featureCounts-flat | # features | 13,690 | 11,955 | 20,092 | 19,318 |
| Â | # incl. genes | 13,690 | 11,955 | 20,092 | 19,318 |
| Â | # bins | 73,745 | 64,787 | 463,496 | 404,205 |
| Â | Tot count | 24,169,605 | 21,986,549 | 82,341,874 | 74,183,344 |
| Â | Tot count/# bins | 327.75 | 339.37 | 177.65 | 183.53 |
featureCounts-exon | # features | 13,937 | 12,138 | 20,410 | 19,552 |
| Â | # incl. genes | 13,937 | 12,138 | 20,410 | 19,552 |
| Â | # bins | 159,182 | 127,516 | 1,069,500 | 855,182 |
| Â | Tot count | 74,482,826 | 59,612,563 | 356,461,786 | 280,317,425 |
| Â | Tot count/# bins | 467.91 | 467.49 | 333.30 | 327.79 |
DEXSeq-default | # features | 13,569 | 11,848 | 19,099 | 18,482 |
| Â | # incl. genes | 13,937 | 12,138 | 20,410 | 19,552 |
| Â | # bins | 75,162 | 65,842 | 478,504 | 415,121 |
| Â | Tot count | 24,608,190 | 22,367,584 | 83,047,366 | 74,720,668 |
| Â | Tot count/# bins | 327.40 | 339.72 | 173.56 | 180.00 |
DEXSeq-noaggreg | # features | 13,709 | 11,969 | 20,147 | 19,353 |
| Â | # incl. genes | 13,709 | 11,969 | 20,147 | 19,353 |
| Â | # bins | 73,981 | 64,927 | 468,722 | 407,779 |
| Â | Tot count | 24,015,599 | 21,873,688 | 81,568,776 | 73,488,445 |
| Â | Tot count/# bins | 324.62 | 336.90 | 174.02 | 180.22 |
SplicingGraph | # features | 5,437 | 4,265 | 16,854 | 15,956 |
| Â | # incl. genes | 5,437 | 4,265 | 16,854 | 15,956 |
| Â | # bins | 87,400 | 70,987 | 737,058 | 647,915 |
| Â | Tot count | 22,311,721 | 18,777,082 | 100,549,202 | 86,827,817 |
| Â | Tot count/# bins | 255.28 | 264.51 | 136.42 | 134.01 |
TopHat-junctions | # features | 11,663 | 10,306 | 18,918 | 18,355 |
| Â | # incl. genes | 11,663 | 10,306 | 18,918 | 18,355 |
| Â | # bins | 56,670 | 50,413 | 290,956 | 266,070 |
| Â | Tot count | 6,542,180 | 6,048,594 | 31,447,564 | 29,616,532 |
| Â | Tot count/# bins | 115.44 | 119.98 | 108.08 | 111.31 |
MISO | # features | 5,259 | 4,153 | 12,767 | 12,225 |
| Â | # incl. genes | 5,259 | 4,153 | 12,767 | 12,225 |
| Â | # bins | 29,371 | 22,040 | 280,521 | 214,608 |
| Â | Tot count | 11,163,878 | 9,535,328 | 35,387,627 | 32,451,761 |
| Â | Tot count/# bins | 380.10 | 432.64 | 126.15 | 151.21 |