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

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#!/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

使用 FastQC 做质控
https://occdn.limour.top/1958.html
Author
Limour
Posted on
July 4, 2022
Licensed under