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Table 1 Number and percentage (xenobiotic reads/DE transcripts) of non-target reads predicted to be differentially expressed (DE). Non-targets were identified in the differentially expressed transcripts assembled using de novo methods (Trinity de novo and SOAPdenovo–Trans). These were represented only in the cDNA libraries of infected or highly infected hosts

From: The influence of trematode parasite burden on gene expression in a mammalian host

Software

Number of S. mansoni sequences in DE genes (Percentage)

UH Down

UH Up

UL Down

UL Up

LH Down

LH Up

DESeq2

 Trinity de novo

0

28 (1 %)

0

0

0

0

 SOAPdenovo–Trans

0

43 (1.2 %)

0

5 (0.3 %)

1 (0.1 %)

3 (0.6 %)

edgeR

 Trinity de novo

0

92 (2.5 %)

0

8 (0.5 %)

0

2 (0.7 %)

 SOAPdenovo–Trans

0

77 (1.8 %)

0

14 (0.6 %)

0

1 (0.2 %)

EBSeq

 Trinity de novo

0

7 (0.3 %)

0

0

0

3 (0.3 %)

 SOAPdenovo–Trans

0

12 (0.3 %)

0

4 (0.2 %)

1 (0.06 %)

9 (0.9 %)

  1. UH: U vs H; UL: U vs L; LH: L vs H
  2. U: Uninfected; L: Low–infected; H: High–infected
  3. Up: Up regulated; Down: Down regulated