<转录组>使用fastp对NCBI下载的SRA数据进行质控

1 、fastp软件的安装

wget http://opengene.org/fastp/fastp

chmod a+x ./fastp

2、数据质控

双端测序

/public/home/ZCH_luxm/software/fastp -i /public/home/ZCH_luxm/NCBI/2_fq/SRR13413579_1.fastq.gz -o /public/home/ZCH_luxm/NCBI/2_fq/SRR13413579_1clean1.fastq.gz -I /public/home/ZCH_luxm/NCBI/2_fq/SRR13413579_2.fastq.gz -O /public/home/ZCH_luxm/NCBI/2_fq/SRR13413579_2clean1.fastq.gz --compression 9

参数设定：

-z 5 设置gzip压缩级别，默认4,1~9 1快-9小

--json 设置输出json文件名

--html 设置输出html文件名

3、批量处理数据(以PBS作业提交服务器）

[ZCH_luxm@login NCBI]$ cat /public/home/ZCH_luxm/NCBI/fastp.pbs

#PBS

#PBS -N fastp

#PBS -l nodes=1:ppn=5

#PBS -q batch

#PBS -o /public/home/ZCH_luxm/NCBI

#PBS -e /public/home/ZCH_luxm/NCBI

#!/bin/bash

for i in 655 868 874 879 918 924;do

{

/public/home/ZCH_luxm/software/fastp -i /public/home/ZCH_luxm/NCBI/2_fq/SRR3823${i}_1.fastq.gz -o /public/home/ZCH_luxm/NCBI/2_fq/SRR3823${i}_1clean.fastq.gz -I /public/home/ZCH_luxm/NCBI/2_fq/SRR3823${i}_2.fastq.gz -O /public/home/ZCH_luxm/NCBI/2_fq/SRR3823${i}_2clean.fastq.gz -h public/home/ZCH_luxm/NCBI/2_fq/SRR3823${i}.hxml -j public/home/ZCH_luxm/NCBI/2_fq/SRR3823${i}.json

}

done

参考链接

https://github.com/OpenGene/fastp#or-download-binary-only-for-linux-systems-httpopengeneorgfastpfastp

https://www.jianshu.com/p/762601f91539