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MISO (Mixture of Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. By modeling the generative process by which reads are produced from isoforms in RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform.

MISO uses the inferred assignment of reads to isoforms to quantitate the abundances of the underlying set of alternative mRNA isoforms. Confidence intervals over estimates can be obtained, which quantify the reliability of the estimates.

Environment Modules

Run module spider miso to find out what environment modules are available for this application.

System Variables

  • HPC_MISO_DIR - installation directory

How To Run

The default configuration file /apps/miso/conf/miso_settings.txt provides fairly conservative settings. Please copy it to apply your modifications and use the


command line switch to point run_miso.py to your custom configuration file.