MISO protocols

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

Download


Versioning


Add your version

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

 (23)
2018
PMCID: 5902843
PMID: 29665865
DOI: 10.1186/s13073-018-0538-1

[…] data [44] and tophat (version 2.0.14) for rna-seq data [45]. 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 [46]. sashimi plots were generated to illustrate all five […]

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

[…] following type of alternative splicing events (fig 1): retained intron (ir), skipped exon (es), alternative 5’donor site (a5), alternative 3’ acceptor site (a3) and mutually exclusive exons (mxe). miso [39] 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: 5336241
PMID: 28257507
DOI: 10.1371/journal.pone.0172950

[…] exclusive exons (mxe). miso [39] 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 for the differential splicing analyses, does not have built-in methods for analysing experimental replicates. as suggested by the authors of miso, we used the pooled samples […]

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

[…] replicates of each condition., miso, which was also used for the differential splicing analyses, does not have built-in methods for analysing experimental replicates. as suggested by the authors of miso, we used the pooled samples for the actual differential splicing test and the individual replicates for filtering as events based on the following 2 rules: 1. only those as events supported […]

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

[…] 2, the within condition psi differences were required to be smaller than the between condition psi differences. finally, as events that met the criteria and for which the compare-sample module of miso returned a bayes factor of at least 5 were considered significant., col-0 rna samples from the 23°c to 16°c temperature experiment were used for cdna synthesis using the bio-rad iscript™ cdna […]

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.

MISO reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review MISO