False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions

Bioinformatics. 2011 Aug 1;27(15):2144-6. doi: 10.1093/bioinformatics/btr354. Epub 2011 Jun 19.


Motivation: Sequencing-based assays such as ChIP-seq, DNase-seq and MNase-seq have become important tools for genome annotation. In these assays, short sequence reads enriched for loci of interest are mapped to a reference genome to determine their origin. Here, we consider whether false positive peak calls can be caused by particular type of error in the reference genome: multicopy sequences which have been incorrectly assembled and collapsed into a single copy.

Results: Using sequencing data from the 1000 Genomes Project, we systematically scanned the human genome for regions of high sequencing depth. These regions are highly enriched for erroneously inferred transcription factor binding sites, positions of nucleosomes and regions of open chromatin. We suggest a simple masking procedure to remove these regions and reduce false positive calls.

Availability: Files for masking out these regions are available at eqtl.uchicago.edu

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Chromatin Immunoprecipitation / methods*
  • Computational Biology / methods
  • Gene Dosage*
  • Genome, Human
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Sequence Analysis / methods*