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author eiriche
date Mon, 03 Dec 2012 03:10:42 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.txt	Mon Dec 03 03:10:42 2012 -0500
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+BSMAP 2.6 Wrapper
+Written by Eugen Eirich @ Institute of Molecular Biology Mainz
+Contact: e.eirich@imb-mainz.de
+
+1. Dependencies
+To use the wrapper, please install BSMAP 2.6 and the Samtools package manually to your dependencies directory.
+
+2. Reference genomes
+You can either use reference genomes from your history or built-in genomes. The built-in genomes are specified
+in the file "bsmap_fasta.loc" in your tool-data directory.
+
+3. WIG parser
+There is a WIG parser included in the repo, which converts the BSMAP Methylation Caller ouptut into WIG format. 
+To use this parser, please first path the file "methratio.py" in your BSMAP directory with the included file
+"methratio.patch":
+
+/path/to/bsmap/methratio.py < methratio.patch
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