Sashimi plots protocols

Sashimi plots specifications


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

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

[…] 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 [46]. 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: 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 [39–41]., 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 […]

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

[…] reads overlap its exons.50 these counts were then used to test for differential expression using negative binomial generalized linear models implemented by the deseq2 r package.51 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 […]

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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