Bsmap: Difference between revisions

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.

@@ Line 10: / Line 10: @@
 |{{#vardefine:testing|}}       <!--PROFILING-->
 |{{#vardefine:faq|}}             <!--FAQ-->
-|{{#vardefine:citation|}}       <!--CITATION-->
+|{{#vardefine:citation|1}}       <!--CITATION-->
 |{{#vardefine:installation|}} <!--INSTALLATION-->
 |}
@@ Line 33: / Line 33: @@
 -->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR
+* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{#uppercase:{{#var:app}}}}_DOC - documentation directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 60: / Line 61: @@
 {{#if: {{#var: citation}}|==Citation==
 If you publish research that uses {{#var:app}} you have to cite it as follows:
-WRITE_CITATION_HERE
+Xi Y, Li W: BSMAP: whole genome Bisulfite Sequence MAPping program. BMC Bioinformatics (2009) 10:232.
 |}}
 <!--Installation-->