Copied the Day2 Folder into our Working Directory ''' cp -r ~/course/data/day2 ~/course/wdir/mapping'''
ls to list files, you can use -l option for more details. The asterisk is a wildcard that denotes "anything" in this folder.
ls ~/course/data/day1/* .
You can work out the size of files in this directory
du -sk ~/course/data/day1/*
piping the output of cat to the word count command with count lines option
zcat file.fastq.gz | wc -l
This calculates reads as each read consists of four lines
zcat file.fastq.gz | awk '{s++}END{print s/4}'
Fastp can be used to trim the adapter files. We also filter out those less than 30 reads.
fastp -i file.fastq.gz -o file.trimmed.fastq -l 30