• 新建一个存放结果的文件夹

mkdir cleandataBase

• 构建脚本前的目录名和样本名文件

ls `pwd`/*_1_val_1.fq.gz > cleandata_fastq_1
ls `pwd`/*_2_val_2.fq.gz > cleandata_fastq_2
find *_1.fq.gz >sample
sed -i "s/_1_val_1.fq.gz/ /g"  sample    #把后缀替换为空格
paste cleandata_fastq_1 cleandata_fastq_2 sample> cleandata_fastq

• 统计clean Base(bp)

vim fc.sh

cat cleandata_fastq|while read id
do
          arr=(${id})
         fq1=${arr[0]}
         fq2=${arr[1]}
         sample=${arr[2]}
fastq-count $fq1 $fq2 >cleandataBase/$sample &
done

• 激活并运行脚本

chmod a+x fc.sh
nohup ./fc.sh

• 把所有结果放在一个文件里面

cat ./JH* >cat_cleandataBase
find JH* >find_cleandataBase
paste find_cleandataBase cat_cleandataBase > cleandataBase

直接提取

cat * > cleandataBase
sed -i  's/}/ /g' cleandataBase
sed -i  's/:/\t/g' cleandataBase
sed -i  's/,/\t/g' cleandataBase
cat cleandataBase | awk '{print $2}' > cleandatabases
cat cleandataBase | awk '{print $4}' > cleandatareads
cat cleandatabases
cat cleandatareads