SpliceTrap: Difference between revisions
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[[Category:Software]][[Category: | [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]] | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|splicetrap}} | |{{#vardefine:app|splicetrap}} | ||
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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--> | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
Latest revision as of 20:44, 12 August 2022
Description
SpliceTrap is a statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing. SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3’/5’ splice sites or Intron Retention. In addition, SpliceTrap can quantify alternative splicing within a single cellular condition, with no need of a background set of reads.
Environment Modules
Run module spider splicetrap to find out what environment modules are available for this application.
System Variables
- HPC_SPLICETRAP_DIR - installation directory
How To Run
The main executable is SpliceTrap
The following databases are available by default:
- hg18
- hg19
- mm9
- rn4