View source for SIPeS

[[Category:Software]][[Category:Biology]][[Category:ChIP-Seq]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|sipes}}
|{{#vardefine:url|http://gmdd.shgmo.org/Computational-Biology/ChIP-Seq/download/SIPeS}}
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|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|}}       <!--CITATION-->
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

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.

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==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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{{#if: {{#var: exe}}|==Additional Information==

WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY

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{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
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{{#if: {{#var: policy}}|==Usage Policy==

WRITE USAGE POLICY HERE (Licensing, usage, access).

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{{#if: {{#var: testing}}|==Performance==

WRITE_PERFORMANCE_TESTING_RESULTS_HERE

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<!--Faq-->
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:

WRITE_CITATION_HERE

|}}
<!--Installation-->
{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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