Download fastq from SRA

原创

JJJJack

修改于 2024-11-20 07:36:51

1241

文章被收录于专栏：生物信息学_troubleshooting生物信息学_troubleshooting

Biowulf has sratoolkit, need to load it before using.

Here is the details:

sinteractive --gres=lscratch:20 --mem=64g --cpus-per-task=24 --time=35:59:00
module load sratoolkit

#download the SRR_Acc_List.txt (sample list) from SRA website
cd /data/$userID/ITP
mkdir sra
nohup cat SRR_Acc_List.txt | while read id; do fasterq-dump -t ./ $id -O ./sra/; done &
#-t ./  will save the tmp downloading files, and will be deleted when the download is finished.
#-O save the output (fastq files, not sra files) in the sra folder.

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