Sashimi plots protocols

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Sashimi plots statistics

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Sashimi plots specifications

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Unique identifier OMICS_07308
Name Sashimi plots
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Sashimi plots

Sashimi plots in pipelines

 (5)
2018
PMCID: 5882894
PMID: 29615706
DOI: 10.1038/s41598-018-23779-4

[…] norway rat reference genome 6.0 using samtools. genome aligned read data were loaded into igv (broad institute), and chromosome locations of exons of interest were determined and used to generate sashimi plots for splice analysis., rt-rcr was performed on cdna prepared from adult rat brain as described previously, using 35 cycles with high-fidelity “platinum” taq polymerase (invitrogen). […]

2018
PMCID: 5902843
PMID: 29665865
DOI: 10.1186/s13073-018-0538-1

[…] from rna-seq data in bam format are used as input for miso (the mixture of isoforms), which detected as events based on bayes factors, filtering criteria, psi values (ψ) and confidence intervals []. sashimi plots were generated to illustrate all five types of as events for visualization. the enrichment of h3k79me2/kb is calculated as the number of reads from h3k79me2 chip-seq data in exon […]

2017
PMCID: 5676891
PMID: 29078298
DOI: 10.1073/pnas.1706502114

[…] them to the species specific reference using gsnap (genomic short-read nucleotide alignment program) (version 2014-05-15, flags -n 1 -t 20 -a sam) (). the remapped reads were then used to generate sashimi plots () in igv (), a graphic display used in rna expression studies to show isoform frequencies by using gapped read information to quantify how often specific introns are skipped. […]

2016
PMCID: 4912119
PMID: 27315173
DOI: 10.1371/journal.pone.0157758

[…] run in two-pass mapping mode to give the most sensitive detection of reads mapping across novel splice junctions. rna-seq output images were generated using the integrative genomics viewer (igv) and sashimi plots [–]., human total rna isolated from a range of adult tissues, including whole brain (pooled from 4 males aged 21–29) and foetal brain (pooled from 21 spontaneously aborted male […]

2016
PMCID: 5117849
PMID: 27775701
DOI: 10.1038/oncsis.2016.63

[…] aligned reads overlap its exons. these counts were then used to test for differential expression using negative binomial generalized linear models implemented by the deseq2 r package. isoform usage (sashimi plots and read coverage) via rna-seq was visualized by plotting alignment data on the integrative genome viewer (broad institute)., all antibodies used, their dilutions and vendor information […]


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Sashimi plots in publications

 (36)
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] a population frequency higher than 1% (popfreq_all >0.01) were filtered out. all somatic mutations called by this procedure were controlled manually using the integrative genomics viewer (igv)., sashimi plots were generated with the r software version 3.4.2 and its packages genomicalignments (1.12.2) and genomicranges (1.28.4) from data downloaded through the gdc portal. expression data […]

PMCID: 5902843
PMID: 29665865
DOI: 10.1186/s13073-018-0538-1

[…] from rna-seq data in bam format are used as input for miso (the mixture of isoforms), which detected as events based on bayes factors, filtering criteria, psi values (ψ) and confidence intervals []. sashimi plots were generated to illustrate all five types of as events for visualization. the enrichment of h3k79me2/kb is calculated as the number of reads from h3k79me2 chip-seq data in exon […]

PMCID: 5861998
PMID: 29478923
DOI: 10.1016/j.devcel.2018.01.022

[…] determined by bootstrapping (n = 1,000). read coverage across exons, introns and splice junctions were normalized and averaged across biological triplicates (and developmental stages) to generate sashimi plots using spladder (). the consensus donor splice sequence (b) was derived from annotated canonical splice junctions detected by ≥10 split reads across all control samples (uninjected […]

PMCID: 5836289
PMID: 29541089
DOI: 10.3389/fpls.2018.00277

[…] program () on the web server using the gtf files generated by cufflinks. differential splicing analysis was done using miso version 0.5.3 () and rmats version 4.0.1 () using the default options. the sashimi plots were generated in order to get the quantitative visualization of the aligned rna-seq reads which enables quantitative comparison of exon usage across the control and treated samples., […]

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

[…] using the normalizequantiles function from the limma 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 […]


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Sashimi plots institution(s)
Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA; Department of Biology, MIT, Cambridge, MA, USA; The Broad Institute of Harvard, MIT, Cambridge, MA, USA; Department of Statistics, Harvard University, Cambridge, MA, USA; Department of Biological Engineering, MIT, Cambridge, MA, USA
Sashimi plots funding source(s)
This work was supported by grant R01 CA-157304 (NIH/NCI) and Starr Cancer Consortium, R01 GM-096193 (NIGMS), IIS-1149662 (NSF), Alfred P. Sloan research fellowship, R01 GM-085319 (NIGMS), U01 CA-184897 (NCI) and R01 HG-002439 (NHGRI).

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