Mercurial > repos > bgruening > bismark
view README @ 16:c066c09db337 draft
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author | bgruening |
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date | Mon, 18 Feb 2013 16:07:12 -0500 |
parents | 221e740377ca |
children | 73508c5b4273 |
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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.