Downloading from GEO

Question

[landscape95]

I am downloading some GSE data sets from GEO NCBI but the speed is too slow 155KB/s, does anyone know other ways to download the raw CEL files? Thank you!

For example this link of GSE9195: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE9195&format=file

Answer 1

[Shicheng Guo]

wget -e robots=off -nH -nd  -r  FTP_URL

FTP_URL is as the following:

ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS1nnn/GDS1001/soft/GDS1001.soft.gz  
ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS1nnn/GDS1001/soft/GDS1001_full.soft.gz  
ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPLnnn/GPL10/soft/GPL10_family.soft.gz   
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSEnnn/GSE1/soft/GSE1_family.soft.gz   
ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPLnnn/GPL10/miniml/GPL10_family.xml.tgz   
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSEnnn/GSE1/miniml/GSE1_family.xml.tgz   
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSEnnn/GSE1/matrix/GSE1_series_matrix.txt.gz   
ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL1nnn/GPL1073/suppl/   
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1000/suppl/GSE1000_RAW.tar   
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1nnn/GSM1137/suppl/GSM1137.CEL.gz  
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1nnn/GSM29nn/suppl/

Answer 2

[Sej Modha]

It seems like that the download speed issue is related to the network you are on as I manage to download the data (~700MB) within two minutes.

Answer 3

[Santosh Anand]

You may try Axel http://www.linuxjournal.com/content/speed-your-downloads-axel

[GenoMax]

Based on the email associated with OP's account the location is Vietnam. This may simply be a case of internet connection connection speed /throttling by the ISP being the limiting factor.

[Santosh Anand]

@genomax I see your point. @landscape, can you see your internet speed by going to http://beta.speedtest.net/ If it reports your dload speed substantially higher than the one you are getting while dloading from GEO, you may try Axel for speeding it up.

Answer 4

[Novogene]

you may try prefetch, which is a tool can download the GEO data quickly. Gene Expression Omnibus Data Mining (IA): Quick and easy download of GEO data

Answer 5

[barslmn]

Aria2 can parallelize your download. https://aria2.github.io/

These parameters seem to work well with GEO: https://stackoverflow.com/a/65650658/7141527