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Table 6 Number of genes where alternative was not detectable

From: Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching

Alignment and isoform switching method Number of genes not detectable
tophat-cuffdiff 4448
tophat-diffsplice 366
tophat-dexseq 109
STAR-cuffdiff 4447
STAR-diffsplice 617
STAR-dexseq 111
  1. The number for cuffdiff is very high because cuffdiff has (with default options) a minimum requirement of 10 reads for a gene locus in order to run the test for isoform switching.