Difference between revisions of "SIPeS"
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
|||
| (3 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category:Biology]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:ChIP-Seq]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|sipes}} | |{{#vardefine:app|sipes}} | ||
| Line 30: | Line 30: | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | < | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| Line 85: | Line 75: | ||
<!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | <!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
| − | |||
| − | |||
Latest revision as of 20:41, 12 August 2022
Description
This module allows you to use SIPeS. With the advent of sequencing techniques, chromatin immunoprecipitation combined with high throughput sequencing (ChIP-Seq) is becoming a powerful tool to study protein-DNA interactions on genome-wide scale.SIPeS (Site Identification from Paired-end Sequencing), a novel algorithm, allows researchers to identify transcript factor binding sites from paired-end sequencing reads. SIPeS uses a dynamic baseline directly through the piling up of fragments to effectively find peaks, overcoming the disadvantage of estimating the average length of DNA fragments from singled-end sequencing achieving more powerful prediction binding sites with high sensitivity and specificity.
Environment Modules
Run module spider sipes to find out what environment modules are available for this application.
System Variables
- HPC_SIPES_DIR - installation directory