Difference between revisions of "SpliceTrap"

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

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]][[Category:NGS]]
+[[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|splicetrap}}
@@ Line 24: / Line 24: @@
 <!--Modules-->
-{{#if: {{#var: mod}}|==Execution Environment and Modules==
+==Environment Modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+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-->
+==System Variables==
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Run-->
 {{#if: {{#var: exe}}|==How To Run==
@@ Line 46: / Line 48: @@
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 <!--Policy-->
-{{#if: {{#var: policy}}|==Usage policy==
+{{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
 |}}