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X-MATE specifications

Information


Unique identifier OMICS_01268
Name X-MATE
Alternative name RNA-MATE
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data UCSC genome browser compatible wiggle plots for genome mapped data, and BED files for exon-junction mapped data.
Input format BED, WIGGLE
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability No
Maintained No

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Publications for X-MATE

X-MATE in publications

 (4)
PMCID: 5705650
PMID: 29184141
DOI: 10.1038/s41598-017-16642-5

[…] water and then used for observation of blood vessels at 3 and 15 minutes after injection. the observation of blood vessel fluorescence was performed using a stereomicroscope (leica)., the µ-ct (scan x mate e090s scanner, comscantechno) was used to collect tomography images of grafted 72 hpf embryos at 3 months after transplantation. samples were fixed with 4% pfa in pbs overnight at room […]

PMCID: 5704663
PMID: 28632647
DOI: 10.1097/BRS.0000000000002266

[…] and siblings were mated to produce ttw mice. male ttw mice were used in the experiments., to observe the process of opll, all samples were examined by micro-computed tomography (micro-ct; scan x-mate-l090, comscantecno, yokohama, japan) before slicing with the source at 75 kvp and 100 ma and the specimen positioned for a magnification of 4.657. micro-ct images were obtained of samples […]

PMCID: 3180702
PMID: 21888672
DOI: 10.1186/1471-2164-12-441

[…] to produce dna sequence reads of 35-50(nt). datasets available via the ncbi short read archive (sra026710)., mapping of solid sequencing reads was performed using a recursive mapping strategy using rna-mate v1.1 [] under default settings. reads were mapped to the mouse genome (mm9) and a library of exon-exon junctions derived from gene models such as refseq, ucsc known genes, ensembl, aceview […]

PMCID: 2896904
PMID: 20625424
DOI: 10.1155/2010/853916

[…] but with the added opportunity of mapping reads that cross splice junctions. in this case, the algorithms differ from whether they require or not junctions's model. algorithms such as erange [] or rna-mate [] require library of junctions constructed using known splice junctions extracted from data-bases and also supplemented with any set of putative splice junctions obtained, for instance, […]


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X-MATE institution(s)
Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
X-MATE funding source(s)
Supported by National Health and Medical Research Council [455857, 456140, 631701]; the Australian Research Council [DP0988754]; the Australian Stem Cell Centre; and the University of Queensland.

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