Some basic stats on our Geoduck methylation data.

Was talking to Steven about some visualization options, and he asked about just some basic information regarding # of Loci, coverage, and other stuff, so I figured that out real quick!

Total number of unique methylated loci sequenced – 5,016,316
Total number of methylated loci with reads in every sample – 611,458
Mean coverage of those 611,000 loci -7.70

Total number of loci with reads in every sample, and at least 10x coverage – 17823
Mean coverage of those 17,000 loci – 48.24

I saved the different files for future use here and the R notebook is here

Also, was playing around with methpipe, which has the ability to identify hypo-methlylated regions (and hyper-methylated regions, with a bit of trickery), so I ran those on the Day10 samples I had completed.

IGV xml cam be found here and the .bed files for the individual samples are located here

igv-hypometh

Advertisements