SpliceTrap: Difference between revisions
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Moskalenko (talk | contribs) m Text replace - "{{#if: {{#var: mod}}|==Execution Environment and Modules== {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}" to "==Required Modules== modules documentation ===Serial=== *{{#var:app}}" |
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==System Variables== | |||
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{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
Revision as of 17:22, 10 August 2012
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.
Required Modules
Serial
- splicetrap
System Variables
- HPC_{{#uppercase:splicetrap}}_DIR - installation directory
How To Run
The main executable is SpliceTrap
The following databases are available by default:
- hg18
- hg19
- mm9
- rn4