Difference between revisions of "MISO"
Moskalenko (talk | contribs) m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]][[Category:RNA-Seq]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|miso}} | |{{#vardefine:app|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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<!--Modules--> | <!--Modules--> | ||
| − | + | ==Environment Modules== | |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | + | ==System Variables== | |
| + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
<!--Run--> | <!--Run--> | ||
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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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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
<!--Policy--> | <!--Policy--> | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#if: {{#var: policy}}|==Usage Policy== |
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) | ||
|}} | |}} | ||
Latest revision as of 20:44, 18 August 2022
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.
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
--settings-filename=SETTINGS_FILENAME
command line switch to point run_miso.py to your custom configuration file.