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Download NCBI GEO dataset

Hi, I am trying to download a dataset with accession number GSEXXXXX from NCBI GEO. I would prefer to use a unix command like wget and to download the fastq files or raw data. Can someone please help, I have gone through other posts but I still can't find an easy way to download the fastq. Thanks!

rna-seq geo gse
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updated by wm wm • written by ATCG ATCG

1 answer

That is a easy way using sra-explorer, as posted above.

Here is another option: If you want to explore the submission on your own, here are some brief info: GEO saved the "processed data", and SRA saved the fastq files.

So, you can get the fastq files from the SRA accession list for the GEO submission, Also, you can find more "processed files" in the GEO page.

  1. Go to the GEO website: https://www.ncbi.nlm.nih.gov/geo/, and search your record (eg: GSE44588)

  2. find "SRA" or "Bioproject" under the Relations section, (eg: SRA SRP018820)

  3. Follow the link SRP018820 to the page, and choose "sent to" ->"Run Selector" -> "Go", then you can find the SRA lists, and corresponding information.

  4. You can find "Accession List" and "Meta data" under the "Select" section, and you can get what you want. (eg: Accession List)

  5. After that, you can download sra files using prefetch, and convert it to fastq files using fastq-dump and fasterq-dump.

    $ prefetch SRR753055
    $ fasterq-dump SRR753055.sra

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written by wm wm

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