Mercurial > repos > bjoern-gruening > bismark

annotate README @ 0:36d124f44c0a draft

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author bjoern-gruening
date Tue, 25 Dec 2012 05:45:46 -0500
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1 Bismark uses Bowtie or Bowtie2 to map the reads.
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2 Create your reference index with bismark_genome_preparation in your
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3 normal Bowtie2/Botwie index directory.
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4 bismark_genome_preparation will create a Bisulfite_Genome folder directly in
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5 your Bowtie2/Bowtie index directory. If you follow that approach you do not
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6 need to specify or modify an extra *.loc file.
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7 That wrapper will extract the path to the Bisulfite_Genome folder from
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8 ./tool-data/bowtie2_indices.loc or ./tool-data/bowtie_indices.loc.