MISO protocols

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MISO specifications

Information


Unique identifier OMICS_01337
Name MISO
Alternative names Mixture of Isoforms, misopy, fastmiso
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An annotation file and a RNA-Seq reads
Input format GFF+SAM
Operating system Unix/Linux
Programming languages C, Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements
numpy, scipy, pysammatplotlib, samtools, bedtools
Maintained Yes

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Documentation


Maintainers


  • person_outline Chris Burge <>
  • person_outline Edoardo Airoldi <>
  • person_outline Yarden Katz <>

Additional information


http://miso.readthedocs.io/en/fastmiso/

Publication for Mixture of Isoforms

MISO in pipelines

 (22)
2018
PMCID: 5902843
PMID: 29665865
DOI: 10.1186/s13073-018-0538-1

[…] data [] and tophat (version 2.0.14) for rna-seq data []. only uniquely mapped reads were used for further downstream analysis., unique reads 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 […]

2017
PMCID: 5336241
PMID: 28257507
DOI: 10.1371/journal.pone.0172950

[…] the following type of alternative splicing events (): retained intron (ir), skipped exon (es), alternative 5’donor site (a5), alternative 3’ acceptor site (a3) and mutually exclusive exons (mxe). miso [] was used to quantify as-events (psi values) in each individual sample and in pooled samples that were generated by merging the replicates of each condition., miso, which was also used […]

2017
PMCID: 5404926
PMID: 28346137
DOI: 10.7554/eLife.23249.063

[…] to rna spike-in controls. exonic, intronic, and intergenic locations were determined using the dm3 gene model., for poly-a and nuclear rna-seq: to analyze annotated alternative splicing, we used miso (), and considered splicing events with a) a bayes score greater than 10 with all replicates combined, b) and consistent directionality of ∆psi in each of the three individual replicates, […]

2017
PMCID: 5431906
PMID: 28232751
DOI: 10.1038/s41467-016-0008-7

[…] using the gsnap aligner. aligned libraries had mate-pair information fixed, were removed of potential pcr duplicates, and sorted using samtools., differential splicing detection was performed using miso using the appropriate configuration for stranded or unstranded rna-seq libraries. as events with a bayes factor < 20, ∆psi < 0.1, 0 reads supporting the inclusion or exclusion isoform, […]

2017
PMCID: 5452352
PMID: 28566089
DOI: 10.1186/s13059-017-1235-x

[…] individual cufflinks results into an overall set of full-length transcripts. custom python scripts were used for detecting the following type of alternative splicing events: ir, es, a5, a3, and mxe. miso software [] was used to quantify as-events (psi values) in each individual sample and in pooled samples that were generated by merging the replicates of each condition. miso, which also used […]


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MISO in publications

 (97)
PMCID: 5955895
PMID: 29769602
DOI: 10.1038/s41598-018-26035-x

[…] transcript isoforms. in this study, we chose salmon, one of the top performers in speed and accuracy based on our internal evaluation, for this type of analysis. tools in the second category include miso, majiq, and rmats, which can be used to analyse rna-seq data at the exon level and to detect known and novel splicing events. these latter methods are especially useful for organisms […]

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

[…] data [] and tophat (version 2.0.14) for rna-seq data []. only uniquely mapped reads were used for further downstream analysis., unique reads 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 […]

PMCID: 5861047
PMID: 29559679
DOI: 10.1038/s41467-018-03326-5

[…] genome hg19 using star aligner. differential gene expression analysis was performed using the deseq2 package, and alternative splicing analysis was performed on pooled star alignments using miso, with hg19 version 2 annotations. events were expression-filtered to require at least one read from each isoform and at least 10 total reads, and significance was determined using the previously […]

PMCID: 5843401
PMID: 29532865
DOI: 10.3892/ijo.2018.4290

[…] from the broad institute (cambridge, ma, usa). enriched gene sets were defined according to the following criteria: p<0.05 and fdr-corrected p-value <0.05. miso () was used to detect rna splicing differences, specifically differentially regulated exons or isoforms., for rt-qpcr, total rna was reverse transcribed to cdna using the superscript iii […]

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

[…] alternative splicing events of each samples were predicted by the astalavista 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 […]


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MISO institution(s)
Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; Department of Biology, MIT, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA; Department of Statistics and FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA; Department of Biological Engineering, MIT, Cambridge, MA, USA
MISO funding source(s)
Supported by grants from the US National Science Foundation and the US National Institutes of Health.

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