16.2.22 Downloading your sequencing data from INCPM servers (done)

Upon sequencing completion you will receive an email detailing two options for downloading your data. 

You may download the sequencing data to your personal computer (PC), Mac or to Unix\Linux based system via your browser or command line.

Browser-based download options

1. Click the Owncloud link to download the Fastq files.
2. Click the Aspera link in the provided email (you will be prompted to install a client software and a browser extension).
3. Copy and paste one of the following URL's to your browser
   • Fastq files - https://stefan.weizmann.ac.il/users/<shortcut-userID>/<userID>/<runID>/
   • Raw Data files - https://stefan.weizmann.ac.il/raw/<runID>/

Command line-based download options 

1. On linux -
   • Click the Super (the Windows) key to open the application launcher on your desktop and then click the terminal icon 
   • Keyboard shortcuts - press the Ctrl + Alt + T key launch the terminal
2. On Mac - open a terminal using one of the following options
   • Click the Launchpad icon  in the Dock, type Terminal in the search field, then click terminal.
   • In the Finder , open the /Applications/Utilities folder, then double-click terminal.
3. On windows - start an application that can open a terminal, such as MobaXterm (may be downloaded from https://mobaxterm.mobatek.net/download.html), and login to the server you wish to download the data onto.

Once you reach the folder in which you wish to place your date, use one of the following commands - 

• Fastq files - wget -nH --cut-dirs=1 -r --reject='index.html*' --exclude-directories=/fastq/<runID>/RawData --no-parent --no-check-certificate https://stefan.weizmann.ac.il/users/<shortcut-userID>/<userID>/<runID>/ (where shortcut-userID consists of the 2 first letters of userID)
• Raw Data files - wget -nH --cut-dirs=1 -r --reject='index.html*' --no-parent --no-check-certificate https://stefan.weizmann.ac.il/raw/<runID>/

If you wish to analyze your data using the UTAP pipeline, you will need to place in your lab's Collaboration folder on the Wexac (the Weizmann Institute's EXAscale) cluster.

Please look at the instructions here in order to place your data in your lab's collaboration folder on Wexac.

You can update your password on susanc at https://susanc3.weizmann.ac.il/bin/prefer 

For questions, contact:

Bioinformatics team: biopipe@weizmann.ac.il