Hello. So I am trying to upload some data directly from the website. Get data → Upload local data → Paste link. Now I am here.
What should I do next so I can process my samples?
Thanks:)
2 Likes
Now you need to find the tool you want to run.
I would recommend running through some of the basic tutorials to get familiar with the interface. https://training.galaxyproject.org/training-material/topics/introduction/
1 Like
When you do as @marten recommended, please be aware that only the first file included in any tar archive is actually uploaded into Galaxy.
If that tar archive contains multiple files, you’ll need to download it locally, unpack it, then upload the files you want to use individually.
FAQ: Loading Data
Right. In other words, Galaxy cannot cash in from that. That’s a bummer. Download it locally is not a solution for now.
1 Like
@Sammy Sorry for the delay, missed your reply.
Hopefully, you have figured this out already, but the individual raw datasets in .cel.gz format are available if you drill down into samples (as supplementary data). Those URLs could be Uploaded to Galaxy and will gz uncompress, but there are no tools wrapped for Galaxy that use .cel data directly as input (is an Affymetrix raw data file format). Or, at least none that I could find.
Example (grouped series): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14334
Example (one of the samples): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM358631
1 Like
2 posts were split to a new topic: Download and Extract Reads in FASTA/Q – times out at NCBI
I am having same problem as I paste the link from tutorial and the file is uploaded but not shown in history