Breadcrumb
Downloading your data from the Genomics Division
If you use Linux, you can follow these instructions:
- Login to your linux terminal and navigate to the directory where you want to store your data
- Locate the HTTP URL for your dataset (should be in the email you received from IIHG Genomics)
- Type the following command: "wget -r -v --no-parent my_http_url_link_from_genomics" (where you substitute the actual link)
- The download should begin and will take several minutes.
- After the download is complete, you will need to move all your fastq files to one folder. So create a new folder called "raw' with the command "mkdir raw"
- Then search for all of the fastq files you just downloaded and move them to the "raw" folder with: "find . -type f -name "*.fastq.gz" -exec mv {} raw \;"
- Now you should have all the fastq files in one folder called "raw." You can use this folder as input to a pipeline or merge fastq files together if they were split across lanes.
If you use Mac OS, you can follow the above directions but you first need to install "wget" on your machine using "Brew":
If you use PC, you should consider switching to Mac or Linux. The IIHG does have a computer lab with Macs available if you do not have access to one.