Downloading multiple samples with GEO accesion numbers

Question

[osiemen]

Dear all,

I have GEO accession numbers for 850 samples I would like to download. What is the easiest way to download a bulk of data from GEO database. I know that it can be done with a ftp or by using R (geoQuery). But I'am not sure how. Can someone please help me or give me advice on how to do this. I am new to this. Here is a link to the paper where the accession numbers can be found in the supplementary : https://academic.oup.com/biostatistics/article/11/2/242/268035?searchresult=1

Example of the accession numbers : GSM20894 GSM20961 GSM20943 GSM20836 GSM20817

Thanks in advance!

Answer 1

[osiemen]

Solution in R:

library(GEOquery)

x <- as.list(scan("files_with_GEO_accesionCodes.txt", what ="" , sep = "" ))

files = lapply(x, getGEOSuppFiles)

[smrutimayipanda]

how do you write the input in file?

Answer 2

[Sej Modha]

A: How to download raw data in batch from NCBI based on Series Accession number or

[osiemen]

Thanks for the link but, unfortunately this doesn't provide enough information to help me out.

[Sej Modha]

Have you tried the solution provided on the post linked above? What is the preferred format of download for the data?

[GenoMax]

osieman52 : That solution is using NCBI unix utilities. You can find more information on those here.

[Sej Modha]

and on the GEO help page.

[osiemen]

I managed to find an easy way to download the files I need by using R.

library(GEOquery) x <- as.list(scan("files_with_GEO_accesionCodes", what ="" , sep = "" )) files = lapply(x, getGEOSuppFiles)

Thank you for the responds!

[osiemen]

A small question added to this quetions, how would one find the batch IDs of the downloaded files? I want to create vectors in orderer to do this I need batch ids. How could I find or generate these batch ids ?

[sparshnegi7]

Were you able to find the solution to making a vector with all the GSM(GEO sample accession numbers)?