Difference between revisions of "SpliceTrap"
Moskalenko (talk | contribs) m (Text replace - "<!--Location--> {{App_Location|app={{#var:app}}|{{#var:ver}}}}" to "") |
Moskalenko (talk | contribs) m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==") |
||
| Line 27: | Line 27: | ||
* 0.90.5 | * 0.90.5 | ||
<!--Modules--> | <!--Modules--> | ||
| − | {{#if: {{#var: mod}}|== | + | {{#if: {{#var: mod}}|==Execution Environment and Modules== |
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | ||
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below--> | <!--Add additional HPC_FOO_BIN and other ENV VARIABLES below--> | ||
Revision as of 02:03, 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.
Available versions
- 0.90.5
Execution Environment and Modules
To use splicetrap with the environment modules system at HPC the following commands are available:
Get module information for splicetrap:
$module spider splicetrap
Load the default application module:
$module load splicetrap
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_SPLICETRAP_DIR - directory where splicetrap is located.
How To Run
The main executable is SpliceTrap
The following databases are available by default:
- hg18
- hg19
- mm9
- rn4