O. lurida RNAseq data fastqc & 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: RNASeq-screening.md
I also tested out the Fastqc program to get another look at the read quality. Here are screen shots from the pre-trimmed read quality:
The 1st “read” from the lane denoted by 0343:
The 2nd “read” from the lane denoted by 0343: