pwd
Course_Materials
, then navigate to the Course_Materials directory using the cd
(change directory) command:cd ~/Course_Materials
ls
to list the contents of the directory. There should be directory called fastqls
to list the contents of the fastq directory:ls fastq
SRR7657883.sra_1.fastq.gz SRR7657883.subset_2M.sra_1.fastq.gz
SRR7657883.sra_2.fastq.gz Test_adapter_contamination.gq.gz.
SRR7657883.subset_2M.sra_2.fastq.gz
You should see two fastq files called SRR7657883.sra_1.fastq.gz and SRR7657883.sra_1.fastq.gz. These are the files for read 1 and read 2 of one of the samples we will be working with.
fastqc fastq/SRR7657883.sra_1.fastq.gz
This creates two files in the fastq directory. The first is the QC report in html format and the second is a zip file containing the data summary data used to generate the report. > \(\Rightarrow\) SRR7657883.sra_1_fastqc.html
> \(\Rightarrow\) SRR7657883.sra_1_fastqc.zip