mkdir -p 00-reads


ls ../RAW/*.gz | cut -d "/" -f3 | cut -d "_" -f1 | sort -u > samples_id.txt

cd 00-reads; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R1*.fastq.gz %_R1.fastq.gz" | bash; cd -
cd 00-reads; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R2*.fastq.gz %_R2.fastq.gz" | bash; cd -

mkdir $(date '+%Y%m%d')_ANALYSIS01_CHARACTERIZATION
