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

Join Date: Jul 2011
Posts: 3,480
Default

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).
dpryan is offline   Reply With Quote