# 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

    1
    2
    3
    4
    5
    6
    7
    8
    9
    10
    11
    12
    13
    14
    15
    16
    17
    18

    #!/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

组织测序
使用 FastQC 做质控
https://occdn.limour.top/1958.html
Author
Limour
Posted on
July 4, 2022
Licensed under
NCBI-GEO：SRA文件转FASTQ文件 Previous
生存分析的基本流程 Next

#### Search

Keyword