FastQC and Trimming - erinvanberkel/EPP622-Test-2 GitHub Wiki

Welcome to the EPP622-Test-2 wiki!

FASTQC

Making a directory for analysis

mkdir evanberk
cd evanberk
mkdir 1_fastqc
cd1_fastqc

Linking datasets

ln -s /pickett_sphinx/teaching/EPP622_2024/test2/raw_data/SRR6922236_1.fastq

Loading and running fastqc

spack load fastqc
fastqc SRR6922236_1

I used secure copy to view the fastqc output on my computer since you can't view it on Sphinx.

scp [email protected]:/pickett_sphinx/teaching/EPP622_2024/test2/analysis/evanberk/1_fastqc/\*html .`

TRIMMING WITH SKEWER

First, I made a new directory called 2_skewer

mkdir 2_skewer
cd 2_skewer

Then I symbolically linked the files to this folder

ln -s /pickett_sphinx/teaching/EPP622_2024/test2/raw_data/SRR6922236_1.fastq

Running skewer

/sphinx_local/software/skewer/skewer \
     -t 2 \
     -l 95 \
     -x AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG \
     -Q 30 SRR6922236_1 \
     -o SRR6922236_1-trimmed.fastq

Now I want to look at the fastqc to see how it changed after trimming

fastqc SRR6922236_1-trimmed.fastq

Copying to my computer

 scp [email protected]:/pickett_sphinx/teaching/EPP622_2024/test2/analysis/evanberk/2_skewer/\*html .

After trimming, there are 48,942 less reads in the the first sample.