RNASEQ分析入门笔记2-下载原始数据

获取原始数据地址

参考文献：AKAP95 regulates splicing through scaffolding RNAs and RNA processing factors. Nat Commun 2016 Nov 8;7:13347. PMID: 27824034

根据文献，原始数据下载地址如下：ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP075/SRP075747， 该目录下共有如下文件：

| 26/May/2016 00:00 | dir | SRR3589948 | |
| 26/May/2016 00:00 | dir | SRR3589949 | |
| 26/May/2016 00:00 | dir | SRR3589950 | |
| 26/May/2016 00:00 | dir | SRR3589951 | |
| 26/May/2016 00:00 | dir | SRR3589952 | |
| 26/May/2016 00:00 | dir | SRR3589953 | |
| 26/May/2016 00:00 | dir | SRR3589954 | |
| 26/May/2016 00:00 | dir | SRR3589955 | |
| 26/May/2016 00:00 | dir | SRR3589956 | |
| 26/May/2016 00:00 | dir | SRR3589957 | |
| 26/May/2016 00:00 | dir | SRR3589958 | |
| 26/May/2016 00:00 | dir | SRR3589959 | |
| 26/May/2016 00:00 | dir | SRR3589960 | |
| 26/May/2016 00:00 | dir | SRR3589961 | |
| 26/May/2016 00:00 | dir | SRR3589962 |

我们只对最后4个来自小鼠的测序数据进行分析，即*59-62.sra

下载文件语法

单个文件下载

本文以下载SRR3589959.sra为例：

wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP075/SRP075747/SRR3589959/SRR3589959.sra

下载过程如下：

--2018-03-21 14:52:21-- ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP075/SRP075747/SRR3589959/SRR3589959.sra
=> 'SRR3589959.sra'
Resolving ftp-trace.ncbi.nlm.nih.gov... 130.14.250.10, 2607:f220:41e:250::12
Connecting to ftp-trace.ncbi.nlm.nih.gov|130.14.250.10|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /sra/sra-instant/reads/ByStudy/sra/SRP/SRP075/SRP075747/SRR3589959 ... done.
==> SIZE SRR3589959.sra ... 1321462823
==> PASV ... done. ==> RETR SRR3589959.sra ... done.
Length: 1321462823 (1.2G) (unauthoritative)
SRR3589959.sra 100%[===================>] 1.23G 3.82MB/s in 11m 8s
2018-03-21 15:03:31 (1.89 MB/s) - 'SRR3589959.sra' saved [1321462823]

文件大小1.2GB，耗时约11Mins

批量下载文件

批量依次下载SRR3589959.sra，SRR3589960.sra，SRR3589961.sra，SRR3589962.sra，四个文件，

for i in ` seq 59 62`;
do
    wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP075/SRP075747/SRR35899${i}/SRR35899${i}.sra  
done

将上述语法保存为*.sh文件，并在终端中执行即可。