Difference between revisions of "SpliceTrap"

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(Created page with "Category:SoftwareCategory:BioinformaticsCategory:GenomicsCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|splicetrap}} |{{#vardefine:url|http://...")
 
 
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[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]][[Category:NGS]]
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[[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|splicetrap}}
 
|{{#vardefine:app|splicetrap}}
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|{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice -->
 
|{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice -->
 
|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice -->
 
|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice -->
|{{#vardefine:exe|}} <!--RUNNING -->
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|{{#vardefine:exe|1}} <!--RUNNING -->
 
|{{#vardefine:conf|}} <!--CONFIGS-->
 
|{{#vardefine:conf|}} <!--CONFIGS-->
 
|{{#vardefine:pbs|}} <!--PBS SCRIPTS-->
 
|{{#vardefine:pbs|}} <!--PBS SCRIPTS-->
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<!--Description-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
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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.
 
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.
<!--Location-->
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{{App_Location|app={{#var:app}}|{{#var:ver}}}}
 
<!--Versions-->
 
==Available versions==
 
* 0.90.5
 
 
<!--Modules-->
 
<!--Modules-->
{{#if: {{#var: mod}}|==Running the application using modules==
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==Environment Modules==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
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==System Variables==
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* 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==
DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY
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The main executable is ''SpliceTrap''
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The following databases are available by default:
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* hg18 
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* hg19
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* mm9 
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* rn4
 
|}}
 
|}}
 
<!--Configuration-->
 
<!--Configuration-->
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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 policy==
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{{#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)
 
|}}
 
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Latest revision as of 20:44, 12 August 2022

Description

splicetrap website  

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