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SRA has done away with SRX experiment directories on FTP site: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/.... might be temporarily down

I have been trying all day to access different SRA files on the GEO database but keep being met with '404' kind of error- stating that the site is down. I have tried on two separate computers and get the same result... taking the following path as an example:

ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX232/SRX2327412

The above path only exists as far as ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/

i.e. there is no 'SRX' directory....

Is it normal for all SRA files on the GEO database to be (temporarily?) inaccessible? If so how long does this tend to last?

software error
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written by chrisclarkson100 chrisclarkson100

SRX is not a valid identifier prefix as far as I can see. The X is most probably a stand-in for eXperiment until an actual P or R or whatever gets assigned, I think.

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written by Ram Ram

3 answers

After contacting SRA. It appears that they have done away with the 'SRX' experiment directory: "The size of the SRA prevents the use of an FTP tree centered around experiments and had to be taken down. If you really need to use the old method of an FTP tree then look at the Runs organized by a study."

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written by chrisclarkson100 chrisclarkson100

Edit the title of this post and put something along the lines of SRA has done away with SRX experiment directories on FTP site. That would make this thread useful to someone searching for a similar issue in future.

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written by GenoMax GenoMax

This dataset is NOT public at this time and that may be the reason.

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written by GenoMax GenoMax

Mysteries of SRA :) Email SRA support and ask them. ENA does not seem to have that data either.

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written by GenoMax GenoMax

You can alternately download directly from the ENA deposit (PRJNA299026, GSE74112),

https://www.ebi.ac.uk/ena/data/view/SRP064924

1) Download the text file generated from ENA/SRA

2) Use the links (column: FASTQ files (FTP)) from the text file to download compressed fastq file (*fastq.gz) (I personally loop over the column to download all files parallel)

The above procedure you can do when the data is public but not accessible directly via GEO repository. If the data is not public you will not have access link in ENA/SRA.

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written by EagleEye EagleEye

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