Previously took the analysis just through the mapping, but didn’t realize Steven wanted me to fully process the data.
So, as en exercise, I followed through with deduplication and sorting of the BAM files.
Then, ran a quick analysis using MethylKit in R. The analysis simply copied what Steven had done with another data set and I haven’t examined it very thoroughly, so am not well-versed on what it’s doing and/or why.
Jupyter Notebook (GitHub):
R Studio Project (download the folder, load project in R Studio, and then run the script in the scripts subdirectory to run the analysis):
Will take the full data sets through this whole pipeline.
In a different experiment compared to when Fidalgo siblings were outplanted at two sites, we also examined Hood Canal (HC) and Oyster Bay (SS/South Sound) grown at Clam Bay (Manchester). Descriptor.
These were the oysters Katherine Silliman spawned in the summer of 2015 and represent seed Jake outplanted years ago.
This was run against the BGI scaffolds >10k.
The results are quite interesting.
The full notebook can be found at https://github.com/sr320/nb-2016/blob/master/O_lurida/BSMAP-06-BGIv001.ipynb.