Difference between revisions of "SIPeS"
Jump to navigation
Jump to search
(Created page with "Category:SoftwareCategory:BiologyCategory:Bioinformatics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|sipes}} |{{#vardefine:url|http://gmdd.shgmo.org/Computa...") |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
||
(One intermediate revision by one other user not shown) | |||
Line 43: | Line 43: | ||
--> | --> | ||
==System Variables== | ==System Variables== | ||
− | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Line 85: | Line 85: | ||
<!--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__ | ||
+ | =Validation= | ||
+ | * Validated 4/5/2018 |
Revision as of 21:24, 6 December 2019
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.
Required Modules
Serial
- sipes
System Variables
- HPC_SIPES_DIR - installation directory
Validation
- Validated 4/5/2018