Difference between revisions of "Bsmap"
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Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:NGSCategory:Methylation {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|bsmap}} |{{#vardefine:url|https://c...") |
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|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine: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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==System Variables== | ==System Variables== | ||
| − | * HPC_{{#uppercase:{{#var:app}}}}_DIR | + | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory |
| + | * HPC_{{#uppercase:{{#var:app}}}}_DOC - documentation directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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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: | ||
| − | + | ||
| + | Xi Y, Li W: BSMAP: whole genome Bisulfite Sequence MAPping program. BMC Bioinformatics (2009) 10:232. | ||
|}} | |}} | ||
<!--Installation--> | <!--Installation--> | ||
Revision as of 02:47, 28 October 2014
Description
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.
Required Modules
Serial
- bsmap
System Variables
- HPC_{{#uppercase:bsmap}}_DIR - installation directory
- HPC_{{#uppercase:bsmap}}_DOC - documentation directory
Citation
If you publish research that uses bsmap you have to cite it as follows:
Xi Y, Li W: BSMAP: whole genome Bisulfite Sequence MAPping program. BMC Bioinformatics (2009) 10:232.