- What you’ll need
- Getting data from SRA
- Accessing data on Basespace
- Downloading fastq files from Basespace
- Downloading raw .bcl files from basespace
There are many times you will need to either access sequence data from public data repositories, like the Sequence Read Archive (SRA), or from your own recent sequencing runs on Illumina's Basespace Cloud service. The steps below outline how to do this from the command line in a way that directly downloads data to our linux server for convenient access to our software
What you’ll need
- A free BaseSpace account with Illumina
- An account on our linux server
- Grabseqs software - if you want to download fastq files from sources other than Basespace, including the Sequence Read Archive (SRA) or MG-RAST
Getting data from SRA
If you just want to get data directly from Illumina's Basespace, you can skip this step!
#navigate to the folder where you want the files to be downloaded grabseqs sra -t 24 -m metadata.csv -r 3 PRJ#######
Accessing data on Basespace
- Connect to our linux server using your terminal or by launching RStudio server in the browser and opening the terminal window.
- Use the illumina basespace client tools and the
bs authfunction to authenticate
bs auth # you should see a message similar to the one below. Open a new browser tab and naviage to the url you see in your terminal. You may be instructed to log into Basespace. Please go to this URL to authenticate: https://basespace.illumina.com/oauth/device?code=NrZBs # Once you've done that, you should see a message in your terminal that welcomes you. Welcome, Daniel Beiting
- Once authenticated, you will be allowed to download data directly from Basespace to our Linux.
- Navigate to your sequencing project on Basespace and locate the project ID in your browser URL
Downloading fastq files from Basespace
Use the project ID number and the
bs download function to get the data.
#specify where you want to data to download using the -o option #NOTE: you need to have privileges to write to the folder you choose bs download project -i 177233056 -o /publicData/myProjectFolder/
- Once the download begins, you will be able to monitor progress in the terminal window (example below)
Downloading raw .bcl files from basespace
In some cases you will want unprocessed .bcl files that Illumina's basespace has not converted to fastq. This is often useful for single cell sequencing experiments. In these cases, you'll download the run, rather than the project
#specify where you want to data to download using the -o option sudo bs download run -i 177233056 -o /publicData/myRunFolder/