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-->
-==Required Modules==
+==Environment Modules==
-[[Modules|modules documentation]]
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-===Serial===
-*{{#var:app}}
-<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
 ==System Variables==
 * HPC_{{uc:{{#var:app}}}}_DIR - installation directory
@@ Line 70: / Line 67: @@
 See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 __NOTOC____NOEDITSECTION__
-=Validation=
-* Validated 4/5/2018