Laura’s Notebook: O. lurida fastq trim testing

Today I downloaded RNASeq data – four fastq files – from Olympia oyster pooled gonad. The gonad was from Fidalgo Bay and Oyster Bay oysters following a 2017 low pH exposure. I unzipped the files, then tested a couple methods of trimming and plotting quality scores for trimmed/untrimmed files.

Jupyter notebook to download/trim files: Inspecting fastq files.ipynb

RMarkdown notebook to run a program to extract and plot quality scores against bp for trimmed/untrimmed files:

from The Shell Game