MapSplice specifications

Information


Unique identifier OMICS_01243
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 2.2.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline MapSplice Team <>

MapSplice article

MapSplice citations

 (4)
2016
PMCID: 5142284

[…] the reads were mapped to the reference rice genome of the michigan state university (msu) rice genome annotation project database (rgap, v7.0) (http://rice.plantbiology.msu.edu/) [26] using mapsplice software [27]. the degseq algorithm [28] was used to filter degs. reads per kilobase of exon model per million mapped reads (rpkm) were used to explore the expression levels of the degs […]

2016
PMCID: 5417364

[…] effect on cell proliferation or apoptosis at 24 h in response to hypoxia (supplementary figure 1). data were aligned and exon structure determined using a multistage pipeline including dexseq,17 mapsplice18 and cufflinks19,20 to identify significant events such as exon skipping and intron retention (supplementary figure 2; supplementary methods). this generated an augmented catalogue […]

2016
PMCID: 4884079

[…] gating criteria. data collected were analyzed using modfit software to discern 2n (g1), s-phase, and 4n (g2 and m) composition., rna-seq reads were mapped to the human genome (build hg19) using the mapsplice informatics tool with default parameters (wang et al., 2010). the mapped reads were further analyzed with cufflinks to calculate the level of gene expression with fpkm (fragments per […]

2015
PMCID: 4656206

[…] and fundamental question., with the continuous decrease of sequencing cost, rna-seq become the most prevalent method for identification of circrnas. although a few bioinformatic algorithms such as mapsplice (wang et al., 2010), tophat-fusion (kim and salzberg, 2011), and ciri (gao et al., 2015) were developed for global discovery of circular rnas, the consistency of these computational tools […]

MapSplice institution(s)
Department of Computer Science, University of Kentucky, Lexington, KY, USA; Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA; Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA; Department of Genetics and UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
MapSplice funding source(s)
Supported by National Science Foundation (grant number 0850237); National Institutes of Health (grant number CA143848 and grant number P20RR016481); Alfred P. Sloan Foundation.

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