Yaamini’s Notebook: Gonad Methylation Analysis Part 3

Quality: controlled

Turns out there was a typo in the IP address I was using to connect to genefish. Whoops. Now that I’m in the office, I was able to complete my FastQC analysis! You can see my process in this Jupyter notebook.

On the Mac mini, I located the files I needed from Owl and ran the command-line version of FastQC. The results can be found in this folder. There are two outputs: an .html file, and a .zip file. The .html files can be viewed by dragging the file from Finder into a web browser. To compare FastQC reports, I ran MultiQC. The interactive .html output can be found here. In general, I think my data has relatively good quality and I can proceed to Bismark.

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Yaamini’s Notebook: Gonad Methylation Analysis

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…

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Yaamini’s Notebook: Gonad Methylation Analysis Part 2

Yaamini vs. Computers

Plan in hand, I went to Roadrunner to start working on my pipeline. Before that, I created a project-virginica-oa repository, and a notebook to detail my pipeline.

However, Roadrunner wasn’t working! Sam had to reboot it a few times. After rebooting, I was unable to open Jupyter Notebook. Sam couldn’t even run any anaconda commands! He rebooted again, but the screen wouldn’t display anything. My struggles are documented in this issue. Steven pointed out that I should transition to the Mac mini in the conference room, so that’s exactly what I did.

But the problems didn’t stop there! In my notebook, I was unable to change the my working directory. In this issue, Sam and Steven pointed out that I need to use exclamation points before commands, and that I shouldn’t comment in the code box itself. By the time I solved all my computer problems, I had to rush to the graduate student town hall. I ensured that I could connect to the Mac mini using the Mac Screen Sharing app, then left. Before I left SAFS, I checked once more that my computer could connect to the Mc mini so I could work from home tonight.

When I got home, my computer could no longer connect to the Mac mini! My guess is that the screen turned off, or someone else tried accessing the computer, preventing me from logging in. So much for starting on my analysis today. I’ll focus on other things and return to this task (hopefully uninterrupted) this weekend.

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