X-MATE: A flexible system for mapping short read data.
David Wood, Qinying Xu, John V. Pearson, Nicole Cloonan, and Sean M. Grimmond
Bioinformatics (2011) 27(4): 580-581
Abstract
A crucial step in the analysis of deep sequencing data is mapping to a reference genome. Accurate and complete mapping greatly enhances the potential discovery of biological results and improves statistical predictions while inaccurate or incomplete mapping may lead to noise and reduced coverage. We recently presented RNA-MATE, a pipeline for the recursive mapping of RNASeq data sets. With the rapid increase in genome resequencing projects, progression of available mapping software and the evolution of file formats, we present X-MATE, an updated version of RNA-MATE, capable of mapping both RNASeq and DNA data sets and with improved performance, output file formats, configuration files, and flexibility in core mapping software.
Supplementary Material
- X-MATE source code. Modules, executables and example configuration files for X-MATE (tar.gz 1.3MB). [Click Here]
- X-MATE user manual. (PDF 2.5MB). [Click Here]
- hg19 Junction Libraries. Exon-junction libraries for hg19 (tar.gz 397MB). [Click Here]
- hg18 Junction Libraries. Exon-junction libraries for hg18 (tar.gz 397MB). [Click Here]
- mm9 Junction Libraries. Exon-junction libraries for mm9 (tar.gz 351MB). [Click Here]
- Testing data (RNA - Mapreads and ISAS). SOLiD test data and configuration files (tar.gz 9.2MB). [Click Here]
- Testing results (RNA - Mapreads). Test results, wiggle plots and BED files for Mapreads RNA (tar.gz 7.2MB). [Click Here]
- Testing results (RNA - ISAS). Test results, wiggle plots and BED files for ISAS RNA (tar.gz 8.9MB). [Click Here]
- Testing data (DNA - ISAS). Illumina test data and configuration file for ISAS DNA mapping (tar.gz 27MB). [Click Here]
- Testing results (DNA - ISAS). Test results, wiggle plots and BED files for ISAS DNA (tar.gz 17MB). [Click Here]
- mapreads v2.4.1 The Applied Biosystems mapping software used in X-MATE. This software is being licensed to you under the OSI compliant GNU Public License (GPL). Please read the license in its entirety and ensure that you understand the licensing conditions for use. Your use of this software indicates your acceptance of this licensing agreement. [Click Here]
- GffToSam The Applied Biosystems utility to convert GFF files to SAM files, packaged with X-MATE, and also available here. This software is being licensed to you under the OSI compliant GNU Public License (GPL). Please read the license in its entirety and ensure that you understand the licensing conditions for use. Your use of this software indicates your acceptance of this licensing agreement.
- ISAS Imagenix Sequence Alignment System optionally used in X-MATE. This software requires a license, details are available here.