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Table 1 Differentially expressed genes detected by multiple analysis pipelines

From: Trimming of sequence reads alters RNA-Seq gene expression estimates

Mapping tool

DE tool

DE Genes, Q40

DE Genes, Q40 L36

TopHat2

Cuffdiff2

1829

150

TopHat2/HTSeq

DESeq

289

2

STAR

DESeq

812

2

RSEM/STAR

DESeq

79

53

STAR

EdgeR

321

0

  1. The number of significantly differentially expressed genes detected, using 5 different analysis pipelines, when comparing the untrimmed data set to the same data set trimmed with SolexaQA, using a quality score of 40 (Q40), or with a quality score of 40 and a minimum length requirement of 36 bases (Q40 L36). DE Tool, differential expression tool. DE Genes, differentially expressed genes