如何对fastq文件进行批量处理

首先进入fastq所在文件夹

#cd /path/to/file

1. 质控

#fastqc -o FASTQC/ -t 8 *.fastq.gz

#multiqc ./

2. 过滤

for i in ls *_combined_R1.fastq.gz; do i=${i/_combined_R1.fastq.gz/};

nohup cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A

AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 30 -m 75 --trim-n --report=minimal -o

${i}_out_R1.fastq.gz -p ${i}_out_R2.fastq.gz ${i}_combined_R1.fastq.gz

${i}_combined_R2.fastq.gz & done

3. 比对

#for i in ls *_out_R1.fastq.gz; do i=${i/_out_R1.fastq.gz/}; nohup hisat2 -p

8 --dta -x /path/to/file/hg19/genome -1 ${i}_out_R1.fastq.gz -2

${i}_out_R2.fastq.gz -S ${i}.sam & done

4. 排序

for i in ls *.sam; do i=${i/.sam/}; nohup samtools sort -@ 8 -o ${i}.bam

${i}.sam & done

5. 计数

#for i in ls *.bam; do i=${i/.bam/}; nohup featureCounts -T 5 -p -t exon -g

gene_id -a /path/to/file/genes.gtf -o ${i}.featureCounts.txt ${i}.bam & done

featureCounts -T 5 -p -t exon -g gene_id -a /path/to/file/genes.gtf -o

all.id.txt *.bam

6.查看后台进程

#jobs / ps

jobs用于查看当前终端后台运行的任务。ps命令用于查看瞬间进程的动态

当然啦，一样的套路也可以用于其他类型测序数据的分析，想要继续学习的同学可以查看往期文章进行回顾并尝试哦~