TelSeq specifications

Information


Unique identifier OMICS_03276
Name TelSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Whole-genome sequencing data
Input format BAM
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
bamtools, GCC
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Zhihao Ding <>

Publication for TelSeq

TelSeq in publications

 (6)
PMCID: 5930419
PMID: 29720177
DOI: 10.1186/s12940-018-0387-9

[…] were localized to other functional domains (fig. ).fig. 2, since pot1 haploin sufficiency has been reported to cause telomere elongation in cll and glioma [], we estimated telomere length via telseq [] and identified a significantly longer age-adjusted mean telomere length in ur-cll tumors compared with un-cll (table and p = 0.009 in fig. )., we further analyzed telomere length […]

PMCID: 5814445
PMID: 29449575
DOI: 10.1038/s41467-017-02688-6

[…] fantom5 hg19 enhancer sites (accession 29/11/2012), and promoter regions derived from version 71 of the ensembl annotation (−2000 to +200 bp of tss) were used. telomere lengths were analyzed using ‘telseq’., sample preparation: pbmcs of t-pll patients (>95% purity of t-cells) and cd3+ t-cells isolated from pb of healthy donors (see “magnetic-bead based cell enrichment“ for details on cell […]

PMCID: 5082821
PMID: 27788131
DOI: 10.1371/journal.pgen.1006385

[…] given biopsy segment by multiplying the number of mutations detected in the exome of the clones derived from the bulk cells by 10 ()., the average length of the telomeric repeats was estimated using telseq []. in newborns, the average length of the telomere restriction fragments (trfs) has been estimated to be approximately 11 kb [, ]. trfs have been shown to contain 1 kb dna […]

PMCID: 5012401
PMID: 27449056
DOI: 10.1534/genetics.116.191148

[…] variant set is available at http://www.andersenlab.org/research/data/cooketal. we used snpeff (version 4.1g) () on this snv set to predict functional effects., telomere lengths were estimated using telseq (version 0.0.1) () on bam files derived from wild isolates or million mutation project (mmp) strain sequencing. to estimate telomere lengths, telseq determines the reads that contain greater […]

PMCID: 4914850
PMID: 27324781
DOI: 10.1038/srep27185

[…] lastly, the candidate sites were also manually inspected using the igv software., whole genome data are mined for reads that are rich in telomere sequence, and relative length is determined. using telseq, we examined the frequency of reads from transgenic and control with different number of copies of ttaggg., to confirm expression of mrna or dna integration, pcr and rt-pcr were carried out. […]


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TelSeq institution(s)
Genome Informatics, Wellcome Trust Sanger Institute, Hinxton, UK; Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; The Center for Human Development and Aging, New Jersey Medical School, Rutgers University, Newark, NJ, USA
TelSeq funding source(s)
Wellcome Trust [WT091310]; Wellcome Trust [WT098051]; European Community's Seventh Framework Programme [FP7/2007–13]; National Institutes of Health [R01HD071180, R01AG030678]

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