Is there an efficient way to bulk-download these GEO datasets at high speed?
GSE134379 (450K) GSE109627 (450K) GSE208623 (EPIC) GSE311578 (EPIC) GSE284764 (EPIC) GSE226298 (EPIC) GSE156984 (EPIC)
This is my first GEO project, so I would appreciate guidance on the most reliable and efficient download approach.
is there also any quick way to capture all the AD and PD related dnam data?
1 answer
You can download the data from accession specific FTP pages. There are different types of files there including a complete data archive (which would be a single file download). If you are on a unix system with direct internet access, you could wget the single archive file below or simply download to a local desktop as an alternative.
e.g. https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE134379 and the RAW data archive for this accession at: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134379/suppl/GSE134379_RAW.tar
You can find files for other accessions from respective pages (for example) :
https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE109627
https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE156984
https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE284764
https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE109627
You could also use a R package like GEOquery as well : https://www.bioconductor.org/packages/release/bioc/html/GEOquery.html
Log in to answer this question.
