MapSplice protocols

View MapSplice computational protocol

MapSplice statistics

You need an account to access this content

info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Read quality control Circular RNA detection Spliced read alignment chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline MapSplice Team <>

Publication for MapSplice

MapSplice in pipelines

 (19)
2018
PMCID: 5805680
PMID: 29422604
DOI: 10.1038/s41467-018-02942-5

[…] normal pancreatic tissue samples (ltg samples) with the ambion mirvana kit was poly-a-enriched and subjected to massively parallel paired-end sequencing (illumina’s hiseq2000/truseq v3 sequencing). mapsplice was used to align reads and rsem (v1.2.14) for gene expression quantification (tpm), using the hg19/grch37-based ucsc “refseq” track for gene annotation. dna for genotyping was isolated […]

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

[…] 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 […]

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 [] using build of 06/06/2014. we selected 275 samples, with 151 primary untreated grade iv gbm samples and 124 […]

2017
PMCID: 5349247
PMID: 28291232
DOI: 10.1038/sdata.2017.24

[…] mrna-seq pipeline (university of north california rna-seq workflow), expression analysis was performed with modifications. first, clean reads were aligned to the human genome reference (hg19) with mapsplice (v2.1.7) , followed by bam file sorting with samtools (v0.1.9) . second, sequencing read counts for each refseq gene were calculated using rsem (v1.2.15) . third, expression levels […]

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, 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 […]

MapSplice in publications

 (119)
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 […]

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 […]

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 […]

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 (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 […]

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 […]

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.

MapSplice reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review MapSplice