Tool: NCBI-SRA File Downloader
NCBI-SRA has stopped direct download of SRA files from their website. I have created a website that might help in getting the required SRA files if the run number is known from the NCBI-SRA website.
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Ram
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sanjay.deshpande •
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sanjay.deshpande •
3 answers
Take SRA112056 as the example, you can download it with the following bash command:
cd /home/shg047/oasis/Holger2016
screen -S SRA112056.Download
wget -r -c -l 2 -nH --cut-dirs=4 ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/
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Ram
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Shicheng Guo
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Shicheng Guo
wget is so slow, you can download it by using aspera software. The more detail information about this method was pasted in my blog: http://blog.sciencenet.cn/blog-1334016-923025.html.
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Ginsea Chen
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Why not just use the NCBI FTP?
Also, I think the documentation for the SRA toolkit is pretty good:
The web interface is a heck of a lot faster than searching through the ftp directories, so that is a plus. My only suggestion to OP would be to return fastq because if you need the sra-toolkit to extract the data then you can just download the file from the command line. In which case, I don't see the real benefit of a web interface.
sra hasn't stopped any type of download. what do you mean? and why download the files when you can manage access with the toolkit which locates data on NCBI servers using accessions. ftp paths are irrelevant.