UCSC LiftOver protocols

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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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Publication for UCSC LiftOver

UCSC LiftOver in pipelines

 (49)
2018
PMCID: 5766238
PMID: 29293496
DOI: 10.1371/journal.pcbi.1005921

[…] 450 level 3 data were downloaded from the broad tcga gdac (http://gdac.broadinstitute.org) using firehose_get. the coordinates of the methylation sites (hg18) were converted into hg38 using the ucsc liftover and further intersected with that of the core promoters (hg38). for each gene, we computed the median of the beta values of the methylation sites present in the core promoter […]

2018
PMCID: 5766238
PMID: 29293496
DOI: 10.1371/journal.pcbi.1005921

[…] and isoforms not detected (no read) in any of the considered samples were removed from the analyses. expression data were log transformed., all sequences were mapped to the hg38 human genome and the ucsc liftover tool was used when necessary. gene tss positions were extracted from gencodev24. utr and cds coordinates were extracted from ensembl biomart. to assign only one 5utr sequence to one […]

2018
PMCID: 5766238
PMID: 29293496
DOI: 10.1371/journal.pcbi.1005921

[…] using ucsc table browser or bedtools getfasta []., tcga isoform tsss were retrieved from https://webshare.bioinf.unc.edu/public/mrnaseq_tcga/unc_hg19.bed and converted into hg38 coordinates with ucsc liftover. for other regulatory regions associated to transcript isoforms (utrs, cds, introns and dfr), we used gencode v24 annotations., the nucleotide (n = 4) and dinucleotide (n = 16) […]

2018
PMCID: 5797088
PMID: 29396444
DOI: 10.1038/s41598-018-20727-0

[…] how relevant the network is to the original list of focus genes., the single tissue cis-eqtl data were downloaded from the gtex website (v6p gtex release, gtex_analysis_v6p_eqtl.tar) using the ucsc liftover tool. then, eqtl snps were located in lncrnas and mrnas using bedtools. fisher’s exact tests were performed using r., for data validation by rt-pcr, human oocyte and cc samples […]

2018
PMCID: 5827201
PMID: 29483551
DOI: 10.1038/s41598-018-21844-6

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


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UCSC LiftOver in publications

 (169)
PMCID: 5943353
PMID: 29743621
DOI: 10.1038/s41598-018-25530-5

[…] control were called using macs software (version 1.4.0rc2) and filtered for peaks with greater than 5-fold enrichment over non-targeting control. peak positions were converted to hg19 using the ucsc liftover tool (https://genome.ucsc.edu/cgi-bin/hgliftover). genomic occupancy peaks were associated with genes within 300 kb using the genomic regions enrichment of annotations tool (great)., […]

PMCID: 5908061
PMID: 29672586
DOI: 10.1371/journal.pgen.1007311

[…] within the window because π = 0 at invariant sites. we also tested 10 chimpanzee [] and 108 macaque [] genomes. additionally, we used our 337-bp sequences of the 46 chimpanzee samples. based on the ucsc liftover tool, we identified chimpanzee (pantro4) and macaque (rhemac3) positions that are orthologous to human (hg19). clr is calculated by multiplying the probabilities of all polymorphic […]

PMCID: 5902498
PMID: 29662110
DOI: 10.1038/s41598-018-24445-5

[…] cell line k562, peripheral blood-derived erythroblasts (pbde) or pbdes in human fetal liver (pbdefetal). the start and end positions were then lifted from hg19 to hg38 coordinates using the ucsc liftover tool with the hg19tohg38 chain file., we used orphanet (http://www.orpha.net/), kegg glycan and pubmed as resources for information on the dispensability of gt genes expressed in rbcs. […]

PMCID: 5887302
PMID: 29688382
DOI: 10.1093/database/bay029

[…] drilling down to specific regions of potential difference represented by off-diagonal points on a plot of 2d est sub-spectra. for example the off-diagonal point that is circled discloses [via the ucsc liftover tool ()] a 1.5 mb rearrangement in umd3 relative to btau4.6.1, with a segment of this length at chr5: 9 500 000 in btau4.6.1 moved to chr5: 104 000 000 in the umd3 assemblies. […]

PMCID: 5885354
PMID: 29618315
DOI: 10.1186/s12864-018-4617-x

[…] from the microcosm target site database []. tfbs were obtained from the study by bickhart et al. [], the tfbs genome positions were converted from bau4.1 assembly to umd3.1 assembly using the ucsc liftover tool and queried the tfbs positions for sequence variants., the dna methylated regions were obtained from the paper by su et al. [] that predicted a bovine dna methylation map using […]


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