Difference between revisions of "SpliceTrap"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:GenomicsCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|splicetrap}} |{{#vardefine:url|http://...") |
|||
| (11 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|splicetrap}} | |{{#vardefine:app|splicetrap}} | ||
| Line 7: | Line 7: | ||
|{{#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 --> | + | |{{#vardefine:exe|1}} <!--RUNNING --> |
|{{#vardefine:conf|}} <!--CONFIGS--> | |{{#vardefine:conf|}} <!--CONFIGS--> | ||
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
| Line 19: | Line 19: | ||
<!--Description--> | <!--Description--> | ||
{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
| − | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | + | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} |
| + | |||
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. | ||
| − | + | ||
| − | |||
| − | |||
| − | |||
| − | |||
<!--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== | ||
| − | + | ||
| + | The main executable is ''SpliceTrap'' | ||
| + | |||
| + | The following databases are available by default: | ||
| + | * hg18 | ||
| + | * hg19 | ||
| + | * mm9 | ||
| + | * rn4 | ||
|}} | |}} | ||
<!--Configuration--> | <!--Configuration--> | ||
| Line 42: | Line 48: | ||
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, 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