Show all answers
Hide all answers
  • What is nG6?

    nG6 is a Next Generation Sequencing data repository allowing to store raw data and associated analyses.

    nG6 uses project, run and analysis levels. A run represents a sequencing unit (e.g. a lane of an Illumina flowcell or a region of a Roche 454 PTP). Analyses are linked to a run, and a project contains one or more runs, as well as analyses.

    nG6 frontend access is restricted by a login form.

    You can learn more about nG6 reading the publication in BMC Genomics.

  • What about user management?

    User access is managed at the project level. Three roles exist : 

    • a "Member" can access and download run and analysis data linked to a project
    • a "Manager" has "Member" rights and can add or remove users from the project he manages (e.g. it allows a researcher to give access to their NGS data to a bioinformatician)
    • an "Administrator" has "Manager" right and can add or remove runs and/or analysis to the project

    Each user can update its contact information and/or password : 

    • connect to ng6
    • enter a project
    • click the "Users" tab
    • check the checkbox of the account to modify
    • click the "Update User" button
    • change the contact information and/or the password in the form
    • click the "Save" button

    If the NGS data was produced on the GeT-PlaGe core facility, the research team login from GeT-PlaGe has to be used to connect to nG6, with the same password (synchronization from GeT-PlaGe database to nG6 database is done every 20 minutes). Please note that for these accounts, the reference database is the one from GeT-PlaGe and the contact information and/or password must be updated connecting to http://get.genotoul.fr/index.php?id=209.

  • How to add a user to my project?

    If you want to give access to your data in nG6 to your colleagues, you can add users : 

    • Connect to ng6 frontend
    • click on "Projects" menu
    • click on the project you want to share
    • click on "Users" tab
    • click on the "Add user" button
    • Fill in the form, for each input of the form (last and first names, login, e-mail), nG6 will suggest a list of account of its database corresponding to the characters you entered
      • if the user you want to add has already an account in nG6, select its account in one of the dropdown boxes
        • nG6 will fill in the whole form as you can check that the account you selected is the one you expected. If you agree, click on the "Add" button
      • if the user you want to add does not have an account in nG6, fill in all he inputs of the form and click on the "Add" button

    Note : an Administrator can add a user with administrator, Manager or Member role. A Manager can add a user with Manager or Member role.

    To remove a user from a project, check the select box of the corresponding user and click on the "Delete user" button

  • How to get my data?

    Several solutions are available : 

    • while accessing your runs/analysis, you can download the files by clicking the available html links in "Download" section, but be aware that if the file is too heavy, the download can take a long time
    • you can go to the "Download" page of this web site > select the data you want to access by clicking the corresponding checkboxes inside the project/run > in the top of the page , next to "Available downloads", select "url", "archive" or "symbolic link", then validate the form with "Download"
      • If you chose "archive", a dialog box asks you your e-mail address. The archive file will be created asynchronously and an e-mail will be sent once done. Warning : The total size of selected data cannot exceed 100 Mo for archive downloading
      • If you chose "url", this workflow will create a list of url of each file of your project. Copy/paste this list in a file "listOfFiles" (Be aware that if the same filename is found in different url, the local file will be overriden) 
        • on your Unix server and use one of the following command to download all the files :
          • wget -i listOfFiles
          • cat listOfFiles | xargs -i curl -O {}
        • On a windows workstation, you can download curl for window (https://curl.haxx.se/download.html), after extracting the archive, run the command  in a windows prompt
          • FOR /F %file in (listOfFiles) DO pathToCurl.exe %file
      • If you chose "symbolic link", a dialog box asks you a login/password couple existing in the Bioinformatics Genotoul platform, as well as a repository where to create the symbolic links in the genotoul server under /work (be sure that you can access in writing mode the repository you specify). The data is then written in one folder per project + one folder per run + one folder par analyze. You can then analyze your data on the genotoul infrastructure or download them. Dowloading the data can be achieved :  
        • From the genologin cluster
          • connect on the Bioinformatics Genotoul server : ssh your_login@genologin.toulouse.inra.fr
          • connect on a node of the cluster : srun --pty bash
          • Run the command : rsync -avLh /work/pathToYourTopFolderWithSymbolicLinks your_server_login@your_server_name:/path_on_your_server
        • From your windows/Mac workstation, use a GUI like FileZilla to transfer your data from genologin.toulouse.inra.fr (cf"Files transfert from/to the platform" FAQ entry on the bioinfo.genotoul.fr website) 

    If you want to create a Bioinformatics Genotoul platform user account, please see http://bioinfo.genotoul.fr/index.php/ask-for/create-an-account/

  • Data storage and security policy

    Your data is stored on a Dell NAS in the INRA campus, replicated once a day on another Dell NAS stored in a datacenter in a distant site.

    Passwords in the database are hashed and the communication between your browser and nG6 is encrypted.

  • How long are my data stored?

    By default, the data (raw data as well as data related to analyzes) added to ng6 is stored during 2 years.

    The team managing your data will contact you when your data exceeds the contractual end of storage date

  • What are the adapter sequences used with Illumina technology?

    When the library insert length is smaller than the sequencing read length, you can find the sequencing adapaters the end of your reads.

    You can find the different sequencing adapters below :

    • TruSeq Adapter - Read 1 : "GATCGGAAGAG-CACACGTCTGAACTCCAGTC"
    • Illumina single End PCR Primer - Read 2 : "GATCGGAAGAG-CGTCGTGTAGGGAAAGAGTG"
    • Nextera  transposase sequence - Read 1 : 5’ TCGTCGGCAGCGTC-AGATGTGTATAAGAGACAG
    • Nextera  transposase sequence - Read 2 : 5’ GTCTCGTGGGCTCGG-AGATGTGTATAAGAGACAG

    You can use cutadapt to remove the adapter sequences, specifying the following sequences : 

    • Nextera index : CTGTCTCTTATACACATCT
    • Illlumina Index : AGATCGGAAGAGC
Copyright © 2013, INRA | Designed by GenoToul Bioinfo, GenoToul Genomic and Sigenae teams | Optimized for