Effects of coverage cutoffutoff values…

Effects of coverage cutoffutoff values on # of DMRs for Day 10 and Day 135 analyses

Spent the morning running the Day 10 and Day 135 analyses again, this time with coverage cutoff values of 3x, 5x and 7x. Each lowering of the cutoff threshold produced ~ twice as many DMRs.

Coverage Cutoff # of DMRs For Day 10 Samples # of DMRs for Day 135 Samples
3x 856 709
5x 300 304
7x 131 136
10x 41 63

I have a directory on scaphapoda with the .bed files, MACAU results files, and boxplots for methylation proportion at each DMR. It can be found here

Code for the different runs are largely cut and paste jobs from the original Day 10 analysis, with cutoff values changed and different file names written. They are Day 135 and Day 10