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Ignoring file size limit when downloading all SRA XML files

Hello,

I'm currently trying to download all SRA files as XML but the file I am downloading is limited to 10 000 experiments (SRX).

Is there any way to ignore this limit ?

xml sra
• 1,623 views • link
updated by GenoMax GenoMax • written by firefox91 • firefox91

Maybe it's a good step to first think what you really need. I respectfully doubt that you need all of the many millions of entries at the SRA. Given that you, again with respect, asked very basic questions towards what sort of data the SRA even contains and how to quantify transcripts, it might be better to simply ask what data you exactly need, so people can suggest a strategy rather than sledgehammer-download the metadata of millions of experiments, the majority probably not even remotely related to your research.

Please elaborate what you need.

• 0 views • link
written by ATpoint ATpoint

1 answer

Since the limit is on NCBI end you don't have any control over that.

When you say you are downloading XML files what do you mean? Just the metadata? NCBI offers various reports in these directories https://ftp.ncbi.nih.gov/sra/reports/ so you may want to download the files from there and parse. They would not be in XML but should get you the entire set.

• 0 views • link
written by GenoMax GenoMax

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