Description

Blacklists of regions with excessive read mapping
This composite track displays genomic regions that are blacklisted due to excessive or anomalous read mapping in sequencing experiments. These regions should be excluded from analyses of ChIP-seq, ATAC-seq, and other functional genomics data to avoid false positive signals.

This track contains two blacklists:

PSU blacklist

A blacklist generated at Penn State University by identifying regions with MACS peaks and high signal windows across multiple ChIP-seq datasets. These regions show consistently high signal regardless of the antibody used, indicating non-specific enrichment.

ENCODE blacklist

The ENCODE blacklist for mm10 (ENCFF547MET), which identifies regions with anomalous, unstructured, or high signal in next-generation sequencing experiments independent of cell line or experiment (Amemiya et al. 2019).

Display Conventions and Configuration

Blacklisted regions are displayed as rectangles along the genome. In "dense" mode, the regions are shown as a compact overview. In "pack" or "full" mode, individual blacklisted intervals are visible.

Methods

The PSU blacklist was generated by identifying genomic regions that are consistently called as peaks by MACS and show high signal windows across multiple ChIP-seq experiments, regardless of the target protein. The ENCODE blacklist was generated using the procedure described in Amemiya et al. (2019).

Credits

Belinda Giardine generated the tracks displayed and developed the track hub.

References

Amemiya HM, Kundaje A, Boyle AP. The ENCODE Blacklist: Identification of Problematic Regions of the Genome. Sci Rep. 2019 Jun 27;9(1):9354. doi: 10.1038/s41598-019-45839-z. PMID: 31249361; PMCID: PMC6597582.

Data Release Policy

These data are available for use without restrictions.

Contact

Ross Hardison rch8@psu.edu