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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.
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BMC Bioinformatics

ISSN: 1471-2105

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