Difference between revisions of "Bismark"
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Moskalenko (talk | contribs) m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|bismark}} | |{{#vardefine:app|bismark}} | ||
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|{{#vardefine:testing|}} <!--TESTING/PROFILING--> | |{{#vardefine:testing|}} <!--TESTING/PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
|} | |} | ||
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Bismark is a bisulfite read mapper and methylation caller. | Bismark is a bisulfite read mapper and methylation caller. | ||
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| − | |||
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<!--Modules--> | <!--Modules--> | ||
| − | + | ==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 | ||
<!--Run--> | <!--Run--> | ||
| + | |||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY | DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY | ||
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
<!--Policy--> | <!--Policy--> | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#if: {{#var: policy}}|==Usage Policy== |
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | ||
|}} | |}} | ||
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{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | + | ||
| + | Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for | ||
| + | Bisulfite-Seq applications. Bioinformatics. 2011 Jun 1;27(11):1571-2. doi: | ||
| + | 10.1093/bioinformatics/btr167. Epub 2011 Apr 14. PubMed PMID: 21493656; PubMed | ||
| + | Central PMCID: PMC3102221. | ||
|}} | |}} | ||
<!--Installation--> | <!--Installation--> | ||
Latest revision as of 18:17, 12 August 2022
Description
Bismark is a bisulfite read mapper and methylation caller.
Environment Modules
Run module spider bismark to find out what environment modules are available for this application.
System Variables
- HPC_BISMARK_DIR - installation directory
Citation
If you publish research that uses bismark you have to cite it as follows:
Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011 Jun 1;27(11):1571-2. doi: 10.1093/bioinformatics/btr167. Epub 2011 Apr 14. PubMed PMID: 21493656; PubMed Central PMCID: PMC3102221.