tDRmapper protocols

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tDRmapper statistics

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tDRmapper specifications

Information


Unique identifier OMICS_10436
Name tDRmapper
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The input into tDRmapper is trimmed small RNA-seq reads.
Biological technology Illumina
Operating system Unix/Linux
Programming languages Perl, R
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Sara R. Selitsky <>

Publication for tDRmapper

tDRmapper in pipeline

2017
PMCID: 5534950
PMID: 28463242
DOI: 10.1038/tp.2017.82

[…] or biological processes at the level of the cell or organism (for example, synaptic transmission). to map, name and quantify trna-derived rnas (tdrs), we analyzed the trimmed reads by using tdrmapper. to predict tdr-targeted genes, we used targetscan v5.0, which allowed us to enter custom small rna sequences two to eight nucleotides in length […]


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tDRmapper in publications

 (5)
PMCID: 5809758
PMID: 29472946
DOI: 10.3389/fgene.2018.00032

[…] differential expression analysis using deseq2 (love et al., ). for tdr analysis, all sized fragments mapping to a single species (e.g., tdr glu-ctc) were summed to a single data point. the program tdrmapper (selitsky and sethupathy, ) was used to determine the size distribution of tdr reads and to further classify tdr species by type of fragmentation (e.g., 5′-trh)., to predict genes […]

PMCID: 5748684
PMID: 29206165
DOI: 10.3390/genes8120366

[…] include: oasis [], chimira [], mirge [], and tiger [], etc. several tools have also been developed to detect isomirs such as seqbuster [], isomirid [] and deanniso []. one trna detection tool, tdrmapper [], is currently available. for other species of srnas, the majority of the alignment-based pipelines would be sufficient for detection given that the annotation is available., the biology […]

PMCID: 5534950
PMID: 28463242
DOI: 10.1038/tp.2017.82

[…] or biological processes at the level of the cell or organism (for example, synaptic transmission). to map, name and quantify trna-derived rnas (tdrs), we analyzed the trimmed reads by using tdrmapper. to predict tdr-targeted genes, we used targetscan v5.0, which allowed us to enter custom small rna sequences two to eight nucleotides in length […]

PMCID: 5832003
PMID: 29657274
DOI: 10.3390/ncrna3010002

[…] of mapping to the genome versus to the trna alone. these concerns arose from the proposal of two different strategies to detect tdrs in 2015: the strategy proposed by telonis et al., and the tdrmapper developed by selitsky and sethupathy. telonis et al. proposed to identify candidate trna-fragment reads by mapping them to the genome, whereas the tdrmapper maps the trimmed reads directly […]

PMCID: 4785646
PMID: 26961774
DOI: 10.1186/s12859-016-0921-0

[…] examine several of the choices that went into the design of tdrmapper, a recently reported tool for identifying transfer rna (trna) fragments in deep sequencing data, evaluate them in the context of currently available knowledge, and discuss their potential […]


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tDRmapper institution(s)
Bioinformatics and Computational Biology Curriculum, University of North Carolina, Chapel Hill, NC, USA

tDRmapper review

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Shailesh Kumar

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Desktop
It's a very good tool to find the tRFs in small RNA-seq datasets. I am loving it.