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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

From: Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage

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