Difference between revisions of "MISO"
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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. | 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. | ||
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| − | + | ==Required Modules== | |
| − | + | [[Modules|modules documentation]] | |
| + | ===Serial=== | ||
| + | *{{#var:app}} | ||
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below--> | <!--Add additional HPC_FOO_BIN and other ENV VARIABLES below--> | ||
| + | ==System Variables== | ||
| + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
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{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
The default configuration file <code>/apps/miso/conf/miso_settings.txt</code> provides fairly conservative settings. Please copy it to apply your modifications and use the | The default configuration file <code>/apps/miso/conf/miso_settings.txt</code> provides fairly conservative settings. Please copy it to apply your modifications and use the | ||
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WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | ||
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | ||
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| + | =Validation= | ||
| + | * Validated 4/5/2018 | ||
Revision as of 21:22, 6 December 2019
Description
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.
Required Modules
Serial
- miso
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
--settings-filename=SETTINGS_FILENAME
command line switch to point run_miso.py to your custom configuration file.
Validation
- Validated 4/5/2018