ce10.blacklist: A 'GRanges' object representing ENCODE signal artefact or...

In GreyListChIP: Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Description

These objects are made from the so-called black list or signal artefact regions defined by Anshul Kundaje and Alan Boyle as part of the ENCODE and modENCODE projects. They are regions which show a signal in essentially any ChIP or similar experiment. For this reason it is useful to remove reads aligning to these regions before carrying out any sort of functional genomics analysis.

These objects can be merged with GreyList objects to perform grey list and black list filtering in one step. They are included in the package as a convenience, with the permission of the creators.

The package includes black lists for worm (ce10, ce11), fly (dm3, dm6), human (hg19, grch37, hg38, grch38), and mouse (mm9, mm10). (Note that hg19 and grch37 differ only in chromosome naming, and likewise for hg38 and grch38.)

Usage

data(ce10.blacklist,package=GreyListChIP)
data(ce11.blacklist,package=GreyListChIP)
data(dm3.blacklist,package=GreyListChIP)
data(dm6.blacklist,package=GreyListChIP)
data(grch37.blacklist,package=GreyListChIP)
data(hg19.blacklist,package=GreyListChIP)
data(grch38.blacklist,package=GreyListChIP)
data(hg38.blacklist,package=GreyListChIP)
data(mm9.blacklist,package=GreyListChIP)
data(mm10.blacklist,package=GreyListChIP)

Format

An S4 GRanges object.

Value

A set of intervals defining the black list regions for the named genome.

Source

https://sites.google.com/site/anshulkundaje/projects/blacklists

References

Amemiya HM, Kundaje A, Boyle AP. The ENCODE blacklist: identification of problematic regions of the genome. Sci Rep. 2019 Dec; 9(1) 9354 DOI: 10.1038/s41598-019-45839-z.

ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.

GreyListChIP documentation built on Nov. 8, 2020, 5:22 p.m.