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Protocols

MapSplice specifications

Information


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

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Documentation


Maintainer


  • person_outline MapSplice Team

Publication for MapSplice

MapSplice citations

 (129)
library_books

An integrated clinical and genomic information system for cancer precision medicine

2018
BMC Med Genomics
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 […]

library_books

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

2018
PMCID: 5880260
PMID: 29610390
DOI: 10.1101/mcs.a002386

[…] 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 reads […]

library_books

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

2018
Nat Commun
PMCID: 5849599
PMID: 29535388
DOI: 10.1038/s41467-018-03099-x

[…] eads 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 (http://broadinstitute.github.io/picard/) was used to assess the alignment profile. SAMtools was used to sort and index the mapped reads and to determine transcriptome co […]

call_split

Improved circRNA Identification by Combining Prediction Algorithms

2018
PMCID: 5844931
PMID: 29556495
DOI: 10.3389/fcell.2018.00020
call_split See protocol

[…] 0.7-fold cutoffs were used. Furthermore, to enable comparison between algorithms, the starting coordinate was converted to 0-based for certain algorithms (ACFS, circRNA_finder, CIRI, CIRI2, DCC, and MapSplice). For de novo prediction, the algorithms with mandatory gene-annotation input (CIRCexplorer2, KNIFE and MapSplice) were provided a mock annotation file to eliminate any annotation-based pred […]

library_books

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

2018
FEBS Open Bio
PMCID: 5881538
PMID: 29632808
DOI: 10.1002/2211-5463.12397

[…] > 5% 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 on th […]

call_split

Silencing of peroxiredoxin II by promoter methylation is necessary for the survival and migration of gastric cancer cells

2018
PMCID: 5903821
PMID: 29422545
DOI: 10.1038/emm.2017.267
call_split See protocol

[…] ethylation27 BeadChip technology (San Diego, CA, USA). Transcriptome data were obtained for 415 patients using RNA-Seq experiments on Illumina HiSeq platforms followed by mRNA quantification with the MapSplice-RSEM pipeline. Correlation values between PRDX2 gene DNA methylation and gene expression values were calculated as the Pearson correlation coefficient using an R package. For Kaplan–Meier su […]

Citations

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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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