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Old 04-04-2016, 06:27 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

How many of the reads get soft-clipped when you use BWA (I'm assuming via bwa-meth)? I think bismark is using end-to-end alignment, which won't work well if you need some soft-clipping (you could alternatively use Trim Galore! beforehand).
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