MISO

Description

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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. Template:App Location

Available versions

• 0.4.4 (fastmiso) - EL6.

Running the application using modules

To use miso with the environment modules system at HPC the following commands are available:

Get module information for miso:

$module spider miso

Load the default application module:

$module load miso

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_MISO_DIR - directory where miso is located.

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

--settings-filename=SETTINGS_FILENAME

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