fastq 批量处理

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派大星在吗

发布于 2021-12-06 13:50:14

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发布于 2021-12-06 13:50:14

文章被收录于专栏：我的技术专刊

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