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


Yaamini’s Notebook: NSA Poster

Here’s the evolution of my poster for NSA!

I tend to have the same evolultion of posters everytime I make them: not enough information for my results in my first draft. Hopefully having this reference will remind me to try and be as specific as possible in my results section the first time!

My first draft:


Steven’s feedback:


Second draft:


Third draft:


Final draft:


from the responsible grad student