title: Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data.
abstract: BACKGROUND
  Adapter trimming and removal of duplicate reads are common practices in next-generation sequencing pipelines. Sequencing reads ambiguously mapped to repetitive and low complexity regions can also be problematic for accurate assessment of the biological signal, yet their impact on sequencing data has not received much attention. We investigate how trimming the adapters, removing duplicates, and filtering out reads overlapping low complexity regions influence the significance of biological signal in RNA- and ChIP-seq experiments.
  
  
  METHODS
  We assessed the effect of data processing steps on the alignment statistics and the functional enrichment analysis results of RNA- and ChIP-seq data. We compared differentially processed RNA-seq data with matching microarray data on the same patient samples to determine whether changes in pre-processing improved correlation between the two. We have developed a simple tool to remove low complexity regions, RepeatSoaker, available at https://github.com/mdozmorov/RepeatSoaker, and tested its effect on the alignment statistics and the results of the enrichment analyses.
  
  
  RESULTS
  Both adapter trimming and duplicate removal moderately improved the strength of biological signals in RNA-seq and ChIP-seq data. Aggressive filtering of reads overlapping with low complexity regions, as defined by RepeatMasker, further improved the strength of biological signals, and the correlation between RNA-seq and microarray gene expression data.
  
  
  CONCLUSIONS
  Adapter trimming and duplicates removal, coupled with filtering out reads overlapping low complexity regions, is shown to increase the quality and reliability of detecting biological signals in RNA-seq and ChIP-seq data.
authors.forename: Mikhail G
authors.initials: MG
authors.lastname: Dozmorov
authors.forename: Indra
authors.initials: I
authors.lastname: Adrianto
authors.forename: Cory B
authors.initials: CB
authors.lastname: Giles
authors.forename: Edmund
authors.initials: E
authors.lastname: Glass
authors.forename: Stuart B
authors.initials: SB
authors.lastname: Glenn
authors.forename: Courtney
authors.initials: C
authors.lastname: Montgomery
authors.forename: Kathy L
authors.initials: KL
authors.lastname: Sivils
authors.forename: Lorin E
authors.initials: LE
authors.lastname: Olson
authors.forename: Tomoaki
authors.initials: T
authors.lastname: Iwayama
authors.forename: Willard M
authors.initials: WM
authors.lastname: Freeman
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Lessard
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Wren
mesh_terms: D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D012313:RNA / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012313:RNA