SpliceMap protocols

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SpliceMap statistics

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SpliceMap specifications

Information


Unique identifier OMICS_01252
Name SpliceMap
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format SAM, BED, WIG
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Additional information


http://web.stanford.edu/group/wonglab/SpliceMap/tutorial.html

Publication for SpliceMap

SpliceMap in pipelines

 (3)
2017
PMCID: 5721832
PMID: 29066438
DOI: 10.1161/JAHA.117.005920

[…] total rna lt kit and sequencing single end reads of 51 bp on a hiseq 2000 (illumina). obtained single‐end rna‐sequencing reads (51 mers) were mapped to the rat genome assembly, version rn4, with splicemap, included in the r/bioconductor package quasr (version 1.8.4) using the following command: qalign(samples.txt, bsgenome.rnorvegicus.ucsc.rn4, splicedalignment=true). using refseq mrna […]

2016
PMCID: 5025045
PMID: 27631780
DOI: 10.1371/journal.pgen.1006313

[…] with the reference genome package (“bsgenome.celegans.ucsc.ce10”) downloaded from bioconductor (https://www.bioconductor.org/) and setting the parameter “splicedalignment = true”, which calls the splicemap aligner with default parameters []. the resulting alignments were converted to bam format, sorted and indexed using samtools [] (version 1.2). expression was quantified on a gene level […]

2014
PMCID: 4278777
PMID: 25565867
DOI: 10.2147/OTT.S72832

[…] adaptors were removed; 2) nucleotides with a quality score <20 were removed; 3) reads with more than 8% nitrogenous bases were removed. all subsequent analyses were based on clean reads., splicemap was used to detect splicing junctions and different types of as events, including exon skipping, mutually exclusive exons, intron retention, 5′as, and 3′as in cscc and atn tissues. the read […]


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SpliceMap in publications

 (18)
PMCID: 5756049
PMID: 29267285
DOI: 10.1371/journal.pgen.1007102

[…] package []. this was necessary since the shapes of the distributions of log2 read counts were different between different samples., to create sashimi plots, rna-seq reads were first realigned using splicemap[], using the quasr function qalign with default value for the alignmentparameter argument, maxhits = 100 and spliced = true., sashimi plots were generated using the sashimi_plot function [] […]

PMCID: 5684781
PMID: 29152379
DOI: 10.1038/cddiscovery.2017.73

[…] against the noncode database and blastn against rfam database to curate a confident set of novel non-coding transcripts. to predict splice junctions, rna-seq data sets were subjected to splicemap using default parameters., we used edger, to normalise tag distribution per library and determined the transcript abundance by mapping reads against the reference genome (ws240). […]

PMCID: 5685475
PMID: 29106373
DOI: 10.7554/eLife.31437.020

[…] was performed using the statistical software r using the quasr package (). sequences were mapped to a reference mouse genome (grcm38/mm10) using splicedalignment = true, which internally uses splicemap () counted per gene (using known gene annotation from ucsc) and normalized to the gene length and library size (rpkm = reads per kilobase transcript and million reads in library). outliers […]

PMCID: 5352092
PMID: 27965457
DOI: 10.18632/oncotarget.13857

[…] (qgf) of the department of biosystems science and engineering (d-bsse) of the eth zurich in basel., single-end rna-seq reads (50-mers) were mapped to the human genome assembly, version hg19, with splicemap ([], included in the r/bioconductor package quasr, version 1.2.2) using the command ‘qalign(“samples.txt”, “bsgenome.hsapiens.ucsc.hg19”, splicedalignment=true)’. using refseq mrna […]

PMCID: 4816419
PMID: 27031341
DOI: 10.1371/journal.pone.0152824

[…] threshold of fdr ≤ 0.001 and an absolute value of log2 ratio ≥ 1., in order to detect alternative splicing evens, we had evaluated a few software for detecting splicing junctions, including tophat, splicemap and mapsplice and soapsplice (version 1.10) []. we selected soapsplice for this work, since it produced the highest call rate (detected true junction number/true junction in total) […]


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SpliceMap institution(s)
Department of Statistics, Stanford University, Stanford, CA, USA; Stanford Genome Technology Center, Palo Alto, CA, USA; Department of Internal Medicine and Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA
SpliceMap funding source(s)
National Institutes of Health (1R01HG004634); Junior faculty grant from the Edward Mallinckrodt Jr. Foundation

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