- #!/bin/sh
- #PBS -N qc
- #PBS -j oe
- #PBS -l ncpus=10
- #PBS -l nodes=1
- #PBS -l mem=20G
- source /home/liuxiangqiong/miniconda3/bin/activate base
- outputdir=${inputpath}/8Fastqc
- #1rawdata_qc
- /cgdata/soft/cellar/iTools_Code20170705/iTools Fqtools stat -InFq ${inputpath}/${sample}_R1.fastq.gz -InFq ${inputpath}/${sample}_R2.fastq.gz -OutStat ${outputdir}/${sample}.stat -CPU 2
- #2fastqc_rawdata
- fastqc ${inputpath}/${sample}_R1.fastq.gz ${inputpath}/${sample}_R2.fastq.gz -o ${outputdir}
- #2fastqc_cleandata
- fastqc ${inputpath}/${sample}_clean_R1.fq.gz ${inputpath}/${sample}_clean_R2.fq.gz -o ${outputdir}
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