Download raw data from BaseSpace

UConn MARS quick guide to getting data off BaseSpace

Yeah! the wet lab processing is done and you have data. You’ve gotten an email from with a link to your project. Clicking that will take you to BaseSpace where you can log in, click on the project tab (folder icon on the top bar), then click “Samples” on the left side of the screen.

If you set up your BaseSpace account with a different email than you use with me, this invite won’t work but I can issue a new invite to whatever address you’d like me to use. If you click the link, log in, and get a message that the link is no longer valid just let me know and I’ll reissue the invite (occasional BaseSpace glitch).

To download your raw data (1 forward and 1 reverse fastq for each sample), select all the samples (if you have more than 25, you will need to select all on each page), then click the download icon.

A download screen will pop up, if this is the first time you are downloading from BaseSpace you will need to Install the Downloader. Then click Download your files.

All of the files from one project will go into a folder, within that folder each sample will be in its own folder, and the actual data will be in Data/Intensities/BaseCalls/. **UPDATE** as of Nov 2016 Illumina changed this file structure and there are no longer “Data/Intensities/BaseCalls/” folders. If you have old and new samples sequenced by MARS, be aware that they will have different file structures. We use the sample barcode to identify each sample so the fastq are named with that barcode, but I tell BaseSpace to use your sample name as the folder name. BaseSpace adds 8 numbers to the end of the project and sample folders that you can just ignore.



If you are analyzing amplicons you might want to check out my mothur batch processing file or my bash file. The batch file has more details of whats happening, the bash file is what I’m actively using on the UConn/UCH HPC1 so there may be slight differences.

If you are analyzing microbial genomes, check out the Computational Biology Core’s tutorial.

If you don’t want to deal with the BaseSpace web interface, you can use BaseMount (a CLI from Illumina). There is a for loop at the top of my bash file for downloading all files for a project and renaming each file with your sample name instead of MARS’ unique identifier for the sample.

Feel free to email, call (860-486-1417), or stop by MARS if you have questions.

Happy Analyzing!!