MISO specifications


Unique identifier OMICS_01337
Alternative name Mixture of Isoforms
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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  • person_outline Chris Burge <>
  • person_outline Edoardo Airoldi <>
  • person_outline Yarden Katz <>

Additional information


MISO article

MISO citations

PMCID: 5336241

[…] 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 […]

PMCID: 4271460

[…] theory behind it., for example, under these criteria, some methods are ruled out for inclusion in this study. e.g., splicetrap [20] only quantifies alternative splicing within a single condition and miso [21] and psginfer [22] do not support biological replicates. our list of programs is not exhaustive; however, we have selected a set of programs which represent a variety of approaches. due […]

PMCID: 4053754

[…] on coverage evidence (that is, quantifying the number of reads supporting each junction and taking the average in case of several splice junctions). for each sample we calculated the overlap with miso (additional file 2 - table s8)., we used cufflinks v1.3.0 [4] to discover novel transcripts in each tissue from the bm dataset and merged all the obtained annotations using cuffmerge. […]

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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