qc质检

for id in *fastq
do
echo $id
# 此处使用8线程，平均每文件处理约10min
fastqc -t 8 $id -o ./out
done

去除接头和低质量序列

conda activate python2.7

for filename in *R1.*fastq
do

# 提取双端公共文件名，并输出检验
base=$(basename $filename R1.raw.fastq) #这一行是提取双端公共文件名，去除了文件名后缀_1.fastq.gz，并将结果保存在变量base中。
echo $base

# 运行去接头程序
trimmomatic PE -threads 9 \\
     ${base}_1.fastq.gz \\
     ${base}_2.fastq.gz \\
     ${base}_1.qc.fq.gz ${base}_s1_se \\
     ${base}_2.qc.fq.gz ${base}_s2_se \\
     ILLUMINACLIP:TruSeq2-PE.fa:2:40:15 \\
     LEADING:2 TRAILING:2 \\
     SLIDINGWINDOW:4:2 \\
     MINLEN:25 
done

for i in HEC2 S185 S186 WT1 WT2 WT3;
do fastq_screen --subset 0 --conf ../my.conf --tag $i
   fastq_screen --subset 0 --filter 001 $i;
done