diff README @ 13:7a143c7b3f1b draft

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+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.