使用 FastQC 做质控

来源

https://anaconda.org/bioconda/fastqc

https://zhuanlan.zhihu.com/p/20731723

https://liripo.github.io/posts/2019/fastqc%E4%BD%BF%E7%94%A8/

通过conda安装纯净环境的FastQC

• conda create -n fastqc -c bioconda fastqc
• conda activate fastqc

批量运行FastQC

#!/bin/sh
#任务名
TASKN=XL1_12
#设置CleanData存放目录
CLEAN=/home/jovyan/upload/22.07.02/$TASKN
#设置qc结果的输出目录
QCDIR=/home/jovyan/upload/22.07.02/fastqc_$TASKN
 
mkdir $QCDIR
 
for file in $CLEAN/*
do
echo $file
SAMPLE=${file##*/}
echo $QCDIR"/"$SAMPLE
mkdir $QCDIR"/"$SAMPLE
fastqc -o $QCDIR"/"$SAMPLE -t 6 `ls $CLEAN/$SAMPLE/*`
done

• nano qc.sh
• chmod +x qc.sh
• ./qc.sh