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Old 08-18-2014, 11:09 PM   #2
frozenlyse
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Location: Australia

Join Date: Sep 2008
Posts: 136
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I wouldnt use bismark on ion torrent data as it is going to have a lot of indels due to homopolymers, and bismark doesnt run bowtie2 in local alignment mode - I would try https://github.com/brentp/bwa-meth as it uses bwa for the alignment - however it may require paired end reads!
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