How do I download my sequencing data?

We do deliver sequencing data via two portals: SLIMS for Illumina data and BioShare for PacBio data.  Both portals offer secure access to the data an support several download protocols.
The emails that will notify you about new sequencing data on SLIMS will contain download instructions.  In BioShare the instructions for several download protocols are integrated in the user interface. BioShare will automatically generate the download commands for you.

Since high throughput sequencing data files tend to be big it is recommended to download the data by running rsync or  wget command line tools (built-in on Unix/Linux/Cygwin). Wget can easily be added to Windows10 as part of bash and is also available for other Windows systems and MACs (multiple install options).  There is also an easy graphical user interface version WGET available for Windows.
The easiest way to add command line UNIX/Linux/BASH functionality (including rsync and wget) to Windows is to install the free MobaXterm terminal from here: https://mobaxterm.mobatek.net/ .
Alternatively you can download files with your webbrowser (clicking the links); since this becomes tedious a download manager would be recommended (e.g for Firefox https://addons.mozilla.org/en-US/firefox/addon/downthemall/ ).

Please see rsync download instructions for SLIMS on this page:  http://bioinformatics.ucdavis.edu/research-computing/documentation/archiving-slims-data/

The wget commands for SLIMS should look like this:

 wget -r -nH -nc -np -R index.html*    "http://slims.bioinformatics.ucdavis.edu/Data/Your_RANDOM_STRING/" &

Please contact the webadmin Adam Schaal for assistance in case of  download problems.


Category: 06 Sequencing Data

← FAQs
Posted in