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X-MATE | A recursive mapping strategy for high-throughput RNA-sequencing data

Provides a pipeline for the recursive mapping of RNA-seq datasets. X-MATE is an updated version of RNA-MATE, capable of mapping both RNA-seq and DNA datasets and with different configuration files. To assist with interrogating the mapped data, X-MATE generates multiple data output formats consistent with commonly used visualization tools such as UCSC genome browser and bioinformatic middleware platforms like Galaxy.

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X-MATE forum

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X-MATE classification

X-MATE specifications

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

X-MATE distribution

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X-MATE support

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Credits

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Publications

Institution(s)

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia

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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