Download sequencing data

After sequencing of your data, all the fastq files and associated analysis files (BAM, etc…) are uploaded on an sftp server. You can either download them using a software with a graphical interface (FileZilla for example), or via a terminal. Both methods are described above.

Using FileZilla (or another software)

If you’re not familiar with the use of command lines, FileZilla is a free and easy to use FTP client alternative in order to download files from a remote server.

In order to fetch the data, you will need to fill in the following fields on the upper bar of the main window:
  • Host :
  • Username : login
  • Password : password given in the QC-Analysis-Report demand in your project
  • Port : 22

Once done, click on QuickConnect to connect to the server. If the connection is successful, a list of files will appears on the right side of the main window. Then, you can select all the files et drag-and-drop them on the directory of your choice (left side of the main window).

Here's an example of a successful connection:

Using a terminal

If you’re used to command lines, the following commands can be used to download the files from the server :

# connection 
$ sftp <login>
$ <enter password>

# see the files available
sftp> ls -l

# fetch all files available 
sftp> get *

# disconnection
sftp> exit

Here's an example of a successful downloading:

[al@dell ~/Documents/fastqs]$ sftp mgx28\
                          Welcome on IGF sftp server  

        The use of this system is restricted to authorized users,
                     unauthorized access is forbidden.
   All information and communications on this system are subject to review, 
      monitoring and recording at any time, without notice or permission.
              Users should have no expectation of privacy.
********************************************************************************* password:  
Connected to  
sftp> get *  
Fetching /home/mgx28/1.fastq.gz to 1.fastq.gz  
Fetching /home/mgx28/2.fastq.gz to 2.fastq.gz  
Fetching /home/mgx28/3.fastq.gz to 3.fastq.gz  
Fetching /home/mgx28/4.fastq.gz to 4.fastq.gz  
Fetching /home/mgx28/md5sum.txt to md5sum.txt  
sftp> exit  
[al@dell ~/Documents/fastqs]$  

Check data integrity

The md5sum tool calculates what we call a file print. This fingerprint, message-digest or checksum is a 128 bits value corresponding to a control sum calculated from a file. This signature is unique to each file. By comparing the MD5 digest of a file to the value supplied that we give you in the md5sum.txt file, you can make sure that the files you downloaded are free from damage and tampering (for example if a network issue have occured).

Under Linux

Under Linux, the md5sum tool is usually integrated to your distribution. You just have to go to the directory containing the files to check, and run the following command:

md5sum -c md5sum.txt

Result has to be "*OK*" for all files.

Under Windows

Under Windows, one can use some softwares like Md5 File Controler or the md5sum tool which is to use in command lines.

Once the file prints are generated, you may compare them to the ones provided in the md5sum.txt file.