登录节点下载sra文件

新建一个txt文档，命名为srr_list.txt

SRR13082339
SRR13082340
SRR13082341
SRR13082342
SRR13082343
SRR13082344
SRR13082345

运行命令

source /public/home/acwnw4bl7y/apprepo/sra_toolkit/3.1.0-none/scripts/env.sh
prefetch srr_list.txt
prefetch --option-file srr_list.txt

放入后台

source /public/home/acwnw4bl7y/apprepo/sra_toolkit/3.1.0-none/scripts/env.sh
nohup prefetch --max-size 100GB SRR13132907 > download.log 2>&1 &

source /public/home/acwnw4bl7y/apprepo/sra_toolkit/3.1.0-none/scripts/env.sh
nohup prefetch --option-file srr_list.txt > download.log 2>&1 &

source /public/home/acwnw4bl7y/apprepo/sra_toolkit/3.1.0-none/scripts/env.sh
cd /public/home/acwnw4bl7y/
ls -d SRR240*/ | while read dir; 
do 
    cd "$dir"
    sra_file="${dir%/}.sra"
    fastq-dump --gzip --split-3 "$sra_file"
    cd ..
done

source /public/home/acwnw4bl7y/apprepo/fastp/0.19.10-gcc731/scripts/env.sh
cd /public/home/acwnw4bl7y/
ls -d SRR240*/ | while read dir; 
do 
    cd "$dir"
    mkdir -p fastp
    fastp -5 20 -i ${dir%/}_1.fastq.gz -I ${dir%/}_1.fastq.gz \
    -o ${dir%/}_1.clean.fq.gz -O ${dir%/}_2.clean.fq.gz \
    -j ./fastp/${dir%/}.json -h ./fastp/${dir%/}.html;
    cd ..
done

source /work/home/acwnw4bl7y/apprepo/hisat2/2.2.1-none/scripts/env.sh
source /work/home/acwnw4bl7y/apprepo/samtools/1.19.2-none/scripts/env.sh
cd /work/home/acwnw4bl7y/DRG
ls -d SRR240*/ | while read dir; 
do 
    cd "$dir"
    hisat2 -t -p 16 -x /work/home/acwnw4bl7y/Rat/Rat \
    -1 ${dir%/}_1.clean.fq.gz -2 ${dir%/}_2.clean.fq.gz \
    2> ${dir%/}.hisat2.log \
    |samtools sort -@ 16 -o ${dir%/}_ht2p.bam
    cd ..
done

module load /public/home/acwnw4bl7y/apprepo/htseq/v2.0.1-none/scripts/htseq-v2.0.1-none
cd /public/home/acwnw4bl7y/SRR24042894
mkdir -p htseq
ls *.bam |while read id;
do 
htseq-count -f bam -s no -i gene_id $id \
/public/home/acwnw4bl7y/Rattus_norvegicus.mRatBN7.2.109.gtf \
1>./htseq/${id%%_*}.txt 2>./htseq/${id%%_*}.HTseq.log;
done