Time to analyze the C. virginica data

Now that my two papers do not require my constant attention, I can start analyzing the MBDSeq data from the C. virginica project. The goal is to see if experimental ocean acidfication drove differential gonad methylation in adult oysters. This lab notebook entry will outline my plan and link to important information I’ll need down the road.

Sam received the FASTQ files and saved them here. The sample IDs follow numerical order, and are non-directional.

Here’s how I will process these samples:

1. FastQC I previously used FastQC with some O. lurida transcriptome data, so I can follow the general steps in this Jupyter notebook.

2. Bismark The purpose of Bismark is to align my sample files with the C. virginica genome, then extract data from methylated areas. I will first test my Bismark pipeline with a subset of one data file. Once I know it works, I will run all my samples.

Now that I know what I’m doing, I should probably do it…