b.limour.top/source/_posts/从eni数据库下载fastq文件.md

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title: 从ENI数据库下载fastq文件 tags: [] id: '2030' categories:

• - uncategorized date: 2022-09-25 14:43:52 ---

进入ENA Browser，搜索对应的GSE号，进入study项目，选择TSV格式的Download report。

从TSV表格中提取下载链接，一行一个写入url.txt，前面加上ftp://，接着使用wget -c -i url.txt下载

来自科研小徐的文章中的批量重命名脚本：

ls *.fastq.gzcut -d '_' -f 1while read i ;do (echo ${i}_1*.gz' will be moved to '${i}_S1_L001_R1_001.fastq.gz);done
ls *.fastq.gzcut -d '_' -f 1while read i ;do (echo ${i}_2*.gz' will be moved to '${i}_S1_L001_R2_001.fastq.gz);done
 
ls *.fastq.gzcut -d '_' -f 1while read i ;do (mv ${i}_1*.gz ${i}_S1_L001_R1_001.fastq.gz;mv ${i}_2*.gz ${i}_S1_L001_R2_001.fastq.gz);done