UCSC LiftOver specifications

Information


Unique identifier OMICS_19501
Name UCSC LiftOver
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Input data A UCSC-generated over.chain file.
Input format BED
Computer skills Basic
Stability Stable
Maintained Yes

Information


Unique identifier OMICS_19501
Name UCSC LiftOver
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

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UCSC LiftOver citations

 (6)
2018
PMCID: 5827201

[…] nuclear variants were obtained from the supporting information of the published whole genome sequence analysis of the 40 patients37. genomic coordinates were converted from hg18 to hg19 using the ucsc liftover tool43; 3419 of 3424 variants were successfully converted. the compiled list of variants consisting of nuclear somatic mutations, mitochondrial somatic mutations and mitochondrial […]

2017
PMCID: 5731425

[…] the bigwig files in human genome assembly hg19 were downloaded. the values at each position were smoothed with a 60-bp window., since the p53 chip clusters are in human genome assembly hg18, the ucsc liftover utility was used along with the hg18-hg19 chain file to convert the sites to their corresponding positions in human genome assembly hg19 to make the profiles., a monte carlo simulation […]

2015
PMCID: 4562498

[…] genome by incorporating the snps and indels into the c57bl/6j genome (rozowsky et al, 2011). the chain file between the two genomes was also reported as an output, which was further used with the ucsc liftover tool. the liftover tool from the ucsc genome browser (kuhn et al, 2013) was applied to get the spret/eij gene annotation. given the genome sequences and the gene annotation, […]

2014
PMCID: 4234490

[…] are available as gff files and as cds and protein sequences in fasta format. we also generated a “chain” file (coordinate mapping between mt3.5 and mt4.0) that can be used in conjunction with the ucsc liftover tool, in order to quickly map any genomic features or annotations from the mt3.5 assembly to the mt4.0 assembly. the release files are available at the jcvi medicago website […]

2013
PMCID: 3597645

[…] peak data from chip-seq experiments of h3k4me3 and h3k27me3 in hela and normal adult dermal fibroblasts (nhdf-ad) were downloaded from ucsc (hg19; broad histone track) and remapped to hg18 by the ucsc liftover tool., chip, library preparation and sequencing were done as described in the supplementary methods. the resulting input chromatin and h3k4me3 and h3k27me3 ip libraries contained ∼64 […]

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