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Old 08-18-2014, 11:41 PM   #3
bioWizz
Junior Member
 
Location: Manipal

Join Date: Jul 2013
Posts: 6
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As you mentioned I had already tried running bowtie2 with local alignment mode, but it did not work.
Just looked into BWA-meth, it does say it supports single end reads. Looks like the tools I was looking for as it employs a similar method as Bismark. Will try to use it and update.
Thank you
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