Importing multiple datasets into one folder
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29 days ago
bart ▴ 20

Hi all,

I want to import multiple FASTQ datasets which can be download from weblinks (from the SRA explorer website) and put all these datasets into one folder, using Galaxy. I have used multiple functions of the ‘upload data’ function in Galaxy EU but I am unable to insert all seperate datasets into one big folder. I want to do this, so I only have to use one tool on one folder and not use one tool on all datasets seperately. I would very much appreciate your help!

Kind regards, Bart

Galaxy • 243 views
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Galaxy specific questions are best asked on their dedicated support forum: https://help.galaxyproject.org/

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Are you interested in moving all .fastq files from various folders into one? Because that can be done with a single command, but not sure that is what you want.

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am unable to insert all seperate datasets into one big folder. 

Doesn't make sense as Galaxy doesn't use folder concept. Instead, it uses datasets, collection lists, collection list of pairs (AFAIK). Probably you meant a single list or single list of pairs.

  1. Create a history
  2. Switch to the newly created history (from step 1) if some other history is active
  3. Download the datasets (data) from URL (web) or from local machine
  4. Now you should see all the imported data in that history
  5. Create a collection with downloaded datasets ( data from step 3). It would be either lists or paired lists depending on the datasets
  6. Run the tool on this collection. This would run a single tool on all the downloaded datasets.

5th step is important. Make sure that the tool takes the lists of datasets (collection).

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