comparison README @ 17:73508c5b4273 draft

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16:c066c09db337

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.

17:73508c5b4273

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.