DU6：记录下载sra数据的几种方法

一、从NCBI获取SRA编号

获取SRA编号

SraAccList.txt

二、用不同方法进行下载

1、aspera下载

#安装
wget http://download.asperasoft.com/download/sw/connect/3.7.4/aspera-connect-3.7.4.147727-linux-64.tar.gz
tar -zxvf aspera-connect-3.7.4.147727-linux-64.tar.gz
sh aspera-connect-3.7.4.147727-linux-64.sh
echo 'export PATH=~/.aspera/connect/bin:$PATH' >> ~/.bashrc
source ~/.bashrc

#下载
ascp -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh -k 1 –T -l 200m [email protected]:/sra/sra-instant/reads/ByRun/sra/SRR/SRR404/SRR4042142/SRR4042142.sra ./SRA_data/
#-i PRIVATE-KEY-FILE             Private-key file name (id_rsa) 
#-k RESUME-LEVEL                 Resume criterion: 0,3,2,1
#-T                              Disable encryption
#-l MAX-RATE                     Max transfer rate

aspera下载速度较快，下载下来为sra格式，需要转换为fastq格式
2、sratoolkit下载

#安装
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.2-1/sratoolkit.2.8.2-1-centos_linux64.tar.gz
tar -zxvf sratoolkit.2.8.2-1-centos_linux64.tar.gz
echo 'export export PATH=~/sratoolkit/sratoolkit.2.8.2-1-centos_linux64/bin/:$PATH' >> ~/.bashrc
source ~/.bashrc

用prefetch工具下载

prefetch -c SRR4042142
#-c|--check-all                   double-check all refseqs

prefetch下载数据为sra格式，在home目录的ncbi文件夹下
用fastq-dump工具下载

fastq-dump -X 5 -Z SRR390728
#-X|--maxSpotId            Maximum spot id
#-Z|--stdout                      Output to stdout, all split data become

fastq-dump下载直接转换为fastq格式
若为双端测序，用fastq-dump --split-3 SRR4042142下载产生两个文件
3、aria2c下载

aria2c -j 20 ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR404/SRR4042142/SRR4042142.sra

并行下载
4、wget下载

wget ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR404/SRR4042142/SRR4042142.sra

三、批量下载

SRA数据下载链接前半部分都一致，只需要修改后面的编号

#/sra/sra-instant/reads/ByRun/sra/{SRR|ERR|DRR}///.sra
for id in `cat SraAccList.txt`
    do ascp -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh -k 1 –T -l 200m [email protected]:/sra/sra-instant/reads/ByRun/sra/{SRR|ERR|DRR}/substr($id,1,6)/$id/$id.sra ./SRA_data/
done

参考链接：
https://www.ncbi.nlm.nih.gov/books/NBK158899/#SRA_download.downloading_sra_data_using