Shelly’s Notebook: May 8, 2019 Geoduck broodstock hemolymph DMR calling

Running methylkit:

I had planned to run MethylKit on Emu’s RStudio web interface to find DMRs in the WGBS hemolymph. In reviewing a previous MethylKit R script, I realized I need sorted bam files, which my initial bismark mox script didn’t include. So I submitted a new mox job to sort my bams. Once the job finishes (after Mox maintenance), I will copy the sorted bams over to gannet and then on to Emu so I can run the Rstudio web interface (a little painful, but getting there!).

Running methylpy

So I thought it might be easier to install methylpy on the server and do DMR calling with this python program instead of with MethylKit in R. Turns out installing this on Mox was too challenging as I kept getting permission denied messages. So I tried installing it on Ostrich which turned out to also be very challenging. Finally, I got it installed and functioning after correctly installing GSL. I am currently running methylpy DMRfind on Ostrich.

from shellytrigg