View source for Bsmap

[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Biology]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|bsmap}}
|{{#vardefine:url|https://code.google.com/p/bsmap/}}
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|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
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|{{#vardefine:citation|1}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

BSMAP is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference. 
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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
* HPC_{{uc:{{#var:app}}}}_DOC - documentation 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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{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
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{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:

Xi Y, Li W: BSMAP: whole genome Bisulfite Sequence MAPping program. BMC Bioinformatics (2009) 10:232.
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{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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