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MapSplice specifications


Unique identifier OMICS_01243
Name MapSplice
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




No version available



  • person_outline MapSplice Team <>

Publication for MapSplice

MapSplice citations


An integrated clinical and genomic information system for cancer precision medicine

PMCID: 5918454
PMID: 29697362
DOI: 10.1186/s12920-018-0347-9

[…] data. we calculate the somatic single nucleotide variants (snvs), insertions and deletions (indels), and copy number variations (cnvs) using mutect [], strelka [], and excavator [], respectively. the mapsplice-rsem [, ] pipeline was used for rna-seq quantification to warrant accuracy in spite of long computation time. galaxy [] pipelines for wes and wts data processing are shown in additional file […]


Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

PMCID: 5910558
PMID: 29678151
DOI: 10.1186/s12864-018-4660-7

[…] to the genome using star [] parameters used were: —outfiltermultimapnmax 7 and —outfiltermismatchnmax 2. annotation free canonical splice-junction mapping was performed, where indicated, with mapsplice 2.0 [] using default parameters., after modifying read ids, ptesfinder v.1 [] was used to screen all reads from each sample for back-splice exon junctions within the gencode v19 human […]


Genomic profiling of dedifferentiated liposarcoma compared to matched well differentiated liposarcoma reveals higher genomic complexity and a common origin

PMCID: 5880260
PMID: 29610390
DOI: 10.1101/mcs.a002386

[…] harmoniously up- or down-regulated in a sample., to reduce false positives (), we applied an integrative analysis of multiple fusion detection methods. we first applied four tools—tophat-fusion (), mapsplice (), fusionmap (), and prada ()—to detect putative fusions in our nine pairs of frozen wd/dd samples. then, fusions with at least one junction read and at least two supporting mate pair […]


Integrative genomic profiling of large cell neuroendocrine carcinomas reveals distinct subtypes of high grade neuroendocrine lung tumors

PMCID: 5849599
PMID: 29535388
DOI: 10.1038/s41467-018-03099-x

[…] of the rna-seq data were all similarly processed to analyze for gene expression profiles. sequencing reads which passed the quality control were mapped to the human reference genome (hg19) using mapsplice. picard tools v1.64 ( was used to assess the alignment profile. samtools was used to sort and index the mapped reads and to determine transcriptome […]


Improved circRNA Identification by Combining Prediction Algorithms

PMCID: 5844931
PMID: 29556495
DOI: 10.3389/fcell.2018.00020

[…] and compared the output from 5 different algorithms (hansen et al., ): circrna_finder (westholm et al., ), circexplorer (zhang et al., ), ciri (gao et al., ), find_circ (memczak et al., ), and mapsplice (wang et al., ). here, this analysis is extended by 6 additional algorithms: acsf (you et al., ), circexplorer2 (zhang et al., ), ciri2 (gao et al., ), dcc (cheng et al., ), knife (szabo et […]


Profiling expression of coding genes, long noncoding RNA, and circular RNA in lung adenocarcinoma by ribosomal RNA‐depleted RNA sequencing

PMCID: 5881538
PMID: 29632808
DOI: 10.1002/2211-5463.12397

[…] ambiguous bases (noted as n), and low‐quality reads containing more than 20 percent of bases with qualities of < 13. the clean reads were then aligned to human genome (version: grch37) using the mapsplice program (v2.1.8). in alignment, preliminary experiments were performed to optimize the alignment parameters (–s 22 –p 12 –ins 6 –del 6 –noncanonical) to provide the largest information […]

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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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