代码语言：javascript复制
批量提交作业
#do_TrimGalore.sh
set -x
/public/software/genomics/unstable/TrimGalore-0.6.1/trim_galore --fastqc --fastqc_args "--outdir ${fastqc}" -o ${output} --stringency 10 --path_to_cutadapt /public/software/anaconda352/envs/py36/bin/cutadapt --phred33 --max_n 10 --length 25 --paired $R1 $R2
set x
#run_TrimGalore.sh bash run_TrimGalore.sh
folder="/public/home/MYL/data/raw_data/EP300-ChIP/"
fastqc="/public/home/MYL/data/clean_data/fastqc"
output="/public/home/MYL/data/clean_data/EP300-ChIP"
mkdir -p ${fastqc}
for file in ${folder}*EP300-U87_R1.fq.gz
do
filename=$(basename $file)
sample=`echo $filename | sed 's/_R1.fq.gz//g'`
R1=${file}
R2=${folder}/${sample}_R2.fq.gz
R1=$R1 R2=$R2 fastqc=$fastqc output=$output < do_TrimGalore.sh sbatch -o ${sample}.Trim.log
sleep 2
done
