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bigBedToBed specifications


Unique identifier OMICS_17344
Name bigBedToBed
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BIGBED
Output format BED
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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bigBedToBed citations


Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates

PLoS Genet
PMCID: 4671654
PMID: 26641089
DOI: 10.1371/journal.pgen.1005686

[…] Great ape CNV data derived from whole genome sequencing (WGS) were downloaded as bigBed files from, and bigBedToBed was used to extract annotations within the region of interest. The human genome hg18 coordinates of the CNV annotations were converted to hg19 coordinates using liftOver with default param […]


Reducing the risk of false discovery enabling identification of biologically significant genome wide methylation status using the HumanMethylation450 array

BMC Genomics
PMCID: 3943510
PMID: 24447442
DOI: 10.1186/1471-2164-15-51

[…] rofiling (GEO GSE40699), as well as genotyping information (GEO GSM999275), for H1-hESC cells generated by the ENCODE production group []. We converted the bigBed files into ASCII bed files using the bigBedToBed method downloaded from the UCSC Genome Browser []. The bed files contained base-by-base methylation information including chromosomal location, and methylated score range from 0 to 100. In […]


ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes

PMCID: 3663758
PMID: 23693142
DOI: 10.1186/1756-8935-6-13

[…] e DNA methylation status of the genomic regions corresponding to Kaiso peaks, a BigBed file for GM12878 WGBS data was downloaded from the UCSC genome browser and was converted to BED format using the BigBedtoBed script available at HOMER [] was then used to plot the percent methylation across Kaiso peak regions using the scrip […]


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