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Table 2 ChIP-seq alignment statistics for different combinations of sequencing data processing steps

From: Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data

Trim Dup RS Total reads properly paired (%) singletons (%) with mate mapped to a different chr (%) SPI1 E-value Number of motifs
- - - 70,929,429 96.81+-1.57 0.40+-0.17 0.80+-0.34 8.2e-9446 44
+ - - 70,155,620 97.49+-1.44 0.15+-0.03 0.39+-0.13 7.6e-10075 65
- + - 40,472,954 95.60+-2.19 0.44+-0.24 1.53+-1.06 1.5e-10726 26
+ + - 40,500,416 96.83+-1.82 0.16+-0.04 0.65+-0.30 4.0e-11010 25
- - 75 68,856,152 96.81+-1.57 0.39+-0.16 0.79+-0.34 2.0e-9425 43
- - 50 68,578,937 96.81+-1.57 0.39+-0.16 0.79+-0.34 2.0e-9425 42
- - 25 68,405,768 96.81+-1.57 0.39+-0.16 0.79+-0.34 2.0e-9425 43
- - 0 68,279,169 96.81+-1.57 0.39+-0.16 0.79+-0.34 2.0e-9425 42
+ - 75 68,004,984 97.50+-1.45 0.15+-0.03 0.38+-0.13 2.8e-9899 64
+ - 50 67,805,679 97.50+-1.45 0.15+-0.03 0.38+-0.13 2.8e-9899 64
+ - 25 67,679,663 97.50+-1.45 0.15+-0.03 0.38+-0.13 2.8e-9899 67
+ - 0 67,587,630 97.50+-1.45 0.15+-0.03 0.38+-0.13 2.8e-9899 62
- + 75 39,242,893 95.61+-2.19 0.43+-0.24 1.51+-1.05 7.6e-10575 26
- + 50 39,080,973 95.61+-2.19 0.43+-0.24 1.51+-1.05 7.6e-10575 26
- + 25 38,981,300 95.61+-2.19 0.43+-0.24 1.51+-1.05 7.6e-10575 26
- + 0 38,908,929 95.61+-2.19 0.43+-0.24 1.51+-1.05 7.6e-10575 26
+ + 75 39,242,893 95.61+-2.19 0.43+-0.24 1.51+-1.05 4.7e-10731 27
+ + 50 39,080,973 95.61+-2.19 0.43+-0.24 1.51+-1.05 4.7e-10731 27
+ + 25 38,981,300 95.61+-2.19 0.43+-0.24 1.51+-1.05 4.7e-10731 27
+ + 0 38,908,929 95.61+-2.19 0.43+-0.24 1.51+-1.05 4.7e-10731 30
  1. "+/-" indicate the step (Trim - adapter trimming, Dup - duplicate removal, RS - filtering out low complexity regions with RepeatSoaker) was applied/not applied, respectively. The RepeatSoaker % reflects the threshold of removing reads overlapping with low complexity regions, i.e., 75% indicates that reads overlapping with low complexity regions 75% or more are removed. SPI1 E-value is an equivalent of a p-value for the detection of PU.1 motif.