Hi,
Thanks for creating this tool, it's very helpful! I had a few questions regarding modifications to the default parameters when dealing with targeted capture data, specifically the Twist Bioscience Methylome kit. I know the defaults are geared towards WGBS, so I thought reducing the maxGap to the mean span of the target regions (~250) might be sensible? Would there be any other considerations to make regarding smoothing etc?
I'm also having some issues with getting the tool to print to standard out in RStudio - the default is verbose = TRUE, but even when explicitly setting this, the tool is running (and completing successfully!) silently.
Thanks,
Michael
Hi,
Thanks for creating this tool, it's very helpful! I had a few questions regarding modifications to the default parameters when dealing with targeted capture data, specifically the Twist Bioscience Methylome kit. I know the defaults are geared towards WGBS, so I thought reducing the maxGap to the mean span of the target regions (~250) might be sensible? Would there be any other considerations to make regarding smoothing etc?
I'm also having some issues with getting the tool to print to standard out in RStudio - the default is verbose = TRUE, but even when explicitly setting this, the tool is running (and completing successfully!) silently.
Thanks,
Michael