android 中cert.sra证书的提取,NCBI下载SRA数据wget 与 fastq-dump

首先采用fastq-dump下载：

除了直接从NCBI下载数据，可以用sra toolkit下载并处理。

1. 下载并安装sra toolkit

http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

选在对应版本下载，我用的是MAC。

下载后点击解压，在终端中，输入：

export PATH=$PATH:/Users/YOU/sratoolkit.2.5.7-mac64/bin

就可以开始使用了。

如果要永久使用，需要在bash_profile添加：

vim  ~/.bash_profile

然后加入：

export PATH=$PATH:/Users/YOU/sratoolkit.2.5.7-mac64/bin

保存退出(Esc, :wq)后：

source ~/.bash_profile

2. 下载SRA数据

找到你想要下载的数据，比如SRP057998

http://www.ncbi.nlm.nih.gov/sra/?term=SRP057998

我只想要下载其中2个数据，SRR2007490和SRR2007493

需要注意的是，必须是 SRR开头！

然后在终端中输入：

prefetch -v SRR2007490

prefetch -v SRR2007493

那么会分别开始下载。下载速度取决于你的网速。

下载的SRA文件会在：

/Users/YOU/ncbi/public/sra/

需要的话，你可以移到自己的文件夹。进入你要移动到的文件夹，输入：

mv /Users/YOU/ncbi/public/sra/SRR2007490.sra

.

mv /Users/YOU/ncbi/public/sra/SRR2007493.sra

.

3. 转换SRA到Fastq

fastq-dump --split-files SRR2007490.sra

fastq-dump --split-files SRR2007493.sra

注意要加 --split-files 参数，要不然只会产生一个fastq文件。而本实验中，是双端测序的。

我使用prefecth下载SRR3656745的时候，由于文件过大32G导致报错：

例子：

####./sratoolkit.2.8.2-1-ubuntu64/bin/prefetch

-v SRR3656745

2017-11-07T02:44:08 prefetch.2.8.2: Using

'ascp'

2017-11-07T02:44:08 prefetch.2.8.2: Using

'ascp'

2017-11-07T02:44:08 prefetch.2.8.2: Using

'/usr/bin/ascp'

2017-11-07T02:44:08 prefetch.2.8.2: Using

'/usr/bin/ascp'

2017-11-07T02:44:09 prefetch.2.8.2:

KClientHttpOpen - connected to www.ncbi.nlm.nih.gov

2017-11-07T02:44:10 prefetch.2.8.2:

KClientHttpOpen - verifying CA cert

2017-11-07T02:44:12 prefetch.2.8.2:

KClientHttpOpen - connected to

sra-download.ncbi.nlm.nih.gov

2017-11-07T02:44:13 prefetch.2.8.2:

KClientHttpOpen - verifying CA cert

2017-11-07T02:44:14 prefetch.2.8.2 warn: Maximum

file size download limit is 20GB

2017-11-07T02:44:14 prefetch.2.8.2: 1)

'SRR3656745' (31GB) is larger than maximum allowed:

skipped

2017-11-07T02:44:14 prefetch.2.8.2: '(null)' is

not recognized as a database or a table

2017-11-07T02:44:15 prefetch.2.8.2:

KClientHttpOpen - connected to

sra-download.ncbi.nlm.nih.gov

2017-11-07T02:44:16 prefetch.2.8.2:

KClientHttpOpen - verifying CA cert

2017-11-07T02:44:17 prefetch.2.8.2:

KClientHttpOpen - connected to

sra-download.ncbi.nlm.nih.gov

2017-11-07T02:44:18 prefetch.2.8.2:

KClientHttpOpen - verifying CA cert

2017-11-07T02:44:19 prefetch.2.8.2:

KClientHttpOpen - connected to

sra-download.ncbi.nlm.nih.gov

2017-11-07T02:44:20 prefetch.2.8.2:

KClientHttpOpen - verifying CA cert

2017-11-07T02:44:21 prefetch.2.8.2:

KClientHttpOpen - connected to

sra-download.ncbi.nlm.nih.gov

2017-11-07T02:44:22 prefetch.2.8.2:

KClientHttpOpen - verifying CA cert

2017-11-07T02:44:24 prefetch.2.8.2:

KClientHttpOpen - connected to

sra-download.ncbi.nlm.nih.gov

2017-11-07T02:44:25 prefetch.2.8.2:

KClientHttpOpen - verifying CA cert

2017-11-07T02:44:27 prefetch.2.8.2:

KClientHttpOpen - connected to

sra-download.ncbi.nlm.nih.gov

2017-11-07T02:44:28 prefetch.2.8.2:

KClientHttpOpen - verifying CA cert

2017-11-07T02:44:29 prefetch.2.8.2:

KClientHttpOpen - connected to

sra-download.ncbi.nlm.nih.gov

2017-11-07T02:44:30 prefetch.2.8.2:

KClientHttpOpen - verifying CA cert

2017-11-07T02:44:31 prefetch.2.8.2: 'SRR3656745'

has no remote vdbcache

Download of some files was skipped because they

are too large

You can

change size download limit by setting

--min-size and --max-size command line

arguments

之后直接使用fastq-dump下载

./sratoolkit.2.8.2-1-ubuntu64/bin/fastq-dump -I

--split-files SRR3656745

使用wget下载，可参考博客：http://blog.sina.com.cn/s/blog_72512a1d0102x9nl.html