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

BMC Bioinformatics

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

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

"+/-" 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.

ISSN: 1471-2105