Can't download files from the ENA (European Nucleotide Archive) site

Question

[Bertalan_Takacs]

Does anybody elso have problems with downloading files from the ENA site? I am following a tutorial, https://ena-docs.readthedocs.io/en/latest/retrieval/ena-project.html and trying to download this project: https://www.ebi.ac.uk/ena/browser/view/PRJEB1787 My problem is, that the "Read files" option on the right, between "Navigation" and "Additional Attributes" simply doesn't show up for me, and because of this I can't download the read files. Does anybody else have a similar problem? How can I fix this? Thanks,

Answer 1

[GenoMax]

Looks like ENA does not have the data links. If you are simply interested in following the tutorial then you can let ENA know about this problem. If you actually want the data then do the following.

Use sra-explorer and search with PRJEB1787. Use directions here: C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks

Remember to use second tab to download from SRA after you add samples you need to your cart. You will have to use fastq(er)-dump from sratoolkit to convert the .sra files. There is over 3 TB of sequence data in this project.

[Bertalan_Takacs]

Thanks, but I try to avoid using SRA because I am not very satisfied of how it handles paired end files. My problem isn't that I can't download this specific project, but that I can't reach any of the run files, even those that I could download earlier.

Answer 2

[Suran]

For anyone who comes here with a similar issue: Please see https://www.ebi.ac.uk/ena/browser/downloading-data for multiple approaches for downloading read files from ENA.