Starting bismark with Manchester data

After evaluating trimgalore output, I decided it’s time to start [bismark](https://github.com/FelixKrueger/Bismark)! To start, I created this script. It’s the same as the one I used for the Hawaii data, but I updated the paths to all the files. I also moved the bisulfite converted genome from the Hawaii data folder to the Manchester data folder. I transferred the script to mox with rsync and it started running…

…only to fail two seconds later. Looking at the slurm output, I saw that it was unable to navigate to bisulfite converted genome:

I navigated to the directory and saw that it was empty! The files must have been on the computer for longer than 30 days before I moved the genome folder from the Hawaii to Manchester subdirectories. I used wget (not curl because mox doesn’t like it) to download the bisulfite converted genome Sam created from this link. I then extracted the files:

tar -xvzf Crassostrea_gigas.oyster_v9.dna_sm.toplevel_bisulfite.tar.gz #Extract (x) and decompress (z) files (f) in a verbose (v) manner

I navigated into the directory to double check that there was actually a bisulfite converted genome inside /gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/. Then, I ran the script. Since I only have eight samples, I’m hoping it’ll finish processing in a week!

Going forward

1. Update the repository README files
2. Write methods
3. Write results
4. Identify DML
5. Determine if RNA should be extracted
6. Determine if larval DNA/RNA should be extracted