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Nucleic Acids Res. 2015 Nov 16;43(20):e133. doi: 10.1093/nar/gkv671. Epub 2015 Jul 10.

Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments.

Author information

1
Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA khmiga@soe.ucsc.edu.
2
Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

Abstract

The human reference assembly remains incomplete due to the underrepresentation of repeat-rich sequences that are found within centromeric regions and acrocentric short arms. Although these sequences are marginally represented in the assembly, they are often fully represented in whole-genome short-read datasets and contribute to inappropriate alignments and high read-depth signals that localize to a small number of assembled homologous regions. As a consequence, these regions often provide artifactual peak calls that confound hypothesis testing and large-scale genomic studies. To address this problem, we have constructed mapping targets that represent roughly 8% of the human genome generally omitted from the human reference assembly. By integrating these data into standard mapping and peak-calling pipelines we demonstrate a 10-fold reduction in signals in regions common to the blacklisted region and identify a comprehensive set of regions that exhibit mapping sensitivity with the presence of the repeat-rich targets.

PMID:
26163063
PMCID:
PMC4787761
DOI:
10.1093/nar/gkv671
[Indexed for MEDLINE]
Free PMC Article

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