view README @ 4:427fb56f2e41 draft default tip

- new options - fixes

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.