--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Tue Dec 25 05:45:46 2012 -0500
@@ -0,0 +1,8 @@
+Bismark uses Bowtie or Bowtie2 to map the reads.
+Create your reference index with bismark_genome_preparation in your
+normal Bowtie2/Botwie index directory. 
+bismark_genome_preparation will create a Bisulfite_Genome folder directly in
+your Bowtie2/Bowtie index directory. If you follow that approach you do not 
+need to specify or modify an extra *.loc file.
+That wrapper will extract the path to the Bisulfite_Genome folder from
+./tool-data/bowtie2_indices.loc or ./tool-data/bowtie_indices.loc.