Back to the C. virginica DMR analysis, plus trying to improve Platanus/Redundans running.
I started a Bismark run for the C. virginia BS-Seq data using
--non_directional argument or Bismark and after hard trimming the first 16 bases off of reads as suggested by Mackenzie. This improved mapping rates significantly, from ~ 8% average to the high 20s. I uploaded the bam files to owl here and notebook here.
After finishing that, I started running the data through some methylation extraction options including
MethylExtract. Having two options should allow me the ability to test a few different options for DMR calling. As of writing the Bismark extraction has finished with data available here and notebook found here
On the subject of Platanus and Redundans, I’ve been trying to get Redundans to do gap closing with the illumina short reads, but for some reason it isn’t able to extract reads from the 50bp reads. Not sure on why this is, but have been experimenting with a few different arguments in Redundans to see if that helps at all. Will update when I’ve found a solution.