MapSplice pipeline

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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  • person_outline MapSplice Team <>

Publication for MapSplice

MapSplice IN pipelines

 (13)
2017
PMCID: 5345226
PMID: 28279210
DOI: 10.1186/s12920-017-0252-7

[…] (2 gbm cells; 3 stem cells) and glioma patient tissue samples (57 samples and 4 normal control samples)., the rest of this section elaborates on these steps., rnaseqv2 level-3 gene expression data (mapsplice and rsem computed) and clinical data were downloaded with tcga assembler [26] using build of 06/06/2014. we selected 275 samples, with 151 primary untreated grade iv gbm samples and 124 […]

2017
PMCID: 5352156
PMID: 28331289
DOI: 10.2147/DDDT.S127889

[…] duplications, and w-mer frequencies. these evaluation metrics were used to understand the nature of the data., raw reads of 50 base pairs or greater that passed filtering were used for mapping. mapsplice,25 an efficient splice junction mapper for rna-seq reads, was used to align the reads and fix gapped alignments. then, a mapping step was used to identify spliced alignments. we applied […]

2017
PMCID: 5356346
PMID: 28304380
DOI: 10.1038/srep44653

[…] supplementary table s5) were obtained from the atlas of non-coding rna in cancer (tanric)54. quality of fastq files was assessed using fastqc and reads were aligned to the human hg19 genome with mapsplice255. transcripts were quantified using rsem56 with 2011 ucsc known gene definitions for protein-coding genes and gencode release 19 for lincrnas. normalization and differential expression […]

2017
PMCID: 5657623
PMID: 29073274
DOI: 10.1371/journal.pone.0185961

[…] with >5% ambiguous bases (noted as n) and low-quality containing >20% bases with a quality of <13. the clean mrna reads were aligned to the bovine genome (version: bos 4.6.1) using the mapsplice program (v2.1.8) [18]. the ebseq algorithm was used to filter the de genes between the steers and bulls groups based on the significant analysis and false discovery rate (fdr) analysis […]

2016
PMCID: 4884079
PMID: 27015110
DOI: 10.7554/eLife.10288.030

[…] 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 […]

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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