UCSC LiftOver pipeline

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 IN pipelines

 (18)
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: 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)29 using the ucsc liftover tool. then, eqtl snps were located in lncrnas and mrnas using bedtools93. 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 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 […]

2018
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)40., […]

2017
PMCID: 5427492
PMID: 28108551
DOI: 10.1534/g3.117.039008

[…] called genotypes, where the fraction is calculated among called genotypes. we converted the ncbi build 36 coordinates in the hapmap data to the grch37 coordinates in the 1000 genomes data using the ucsc liftover (speir et al. 2016) to make the coordinates in the two data sets consistent with each other. to minimize the confounding effect of mismapping, we excluded sites involved in putative […]

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