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Frequently Asked Questions

Contents

  1. Project Info
    1. What is this project?
  2. Database Accounts
    1. How do I acquire an account?
    2. I've forgotten my username and password?
    3. I can't open my account
  3. Biological Samples
    1. What kinds of samples does the database accept, and what attributes are stored?
    2. How do I submit my sample(s) to the database?
    3. How do I enter a multiplexed library into the database?
  4. System questions
    1. How can I find out about the database schema?


  1. Project Info
    1. What is this project?
    2. The HTSEQ project tracks sample data, protocol and analysis parameters, and provides standardized data and reports for high throughput sequencing data. Our project is fairly tightly coupled with the local sequencing-core and is integrated with their utilization of the University's of iLab Portal, primarily importing and processing the Core-handled samples and jobs. After sequencing by the Core (Illumina platforms), the resulting data is automatically processed using the core facility’s pipeline servers. The resulting data are staged on centrally managed network attached storage, and are subsequently processed to yield a standardized, compact data archive. This archive is communicated back to the requestor via HTSEQ web interfaces and made available for analysis using our local Galaxy server. Our system leverages open source tools to report quality control statistics that may uncover issues with either library or assay quality. These standardized data and QC results are made available via web interfaces to users and are easily sharable with both their collaborators and entire lab groups. Further, our flexible data model facilitates the annotation of relationships between the sample and assays. The end result is that the researcher and their collaborators can visualize the overall experimental design, and are able to access all the relevant data within the study.

  2. Database Accounts
    1. How do I acquire an account?
    2. Database accounts are given to only:

      Princeton University Central Authentication Service handles the project's login credentials. Provided you can already authenticate here, and you are one of the above, you may register for an HTSEQ account here. Typically, accounts for the Core's customers are usually sponsored and created by the Core-staff, without the need for independent registration [i.e. they fill and submit the form, for you]. If you are a Princeton researcher, and need to sponsor an external collaborator, please consult the Guest Account Provisioning (GAP) service.

    3. I've forgotten my username and password, and now I can't get in. Could you check on this for me?
    4. Authentication is currently handled through Princeton's CAS. The curators do not know your password, so we can't remind you. Passwords must be retrieved changed through Princeton processes, clicking the "Forgot your password?" link when given the opportunity.

    5. I can't log in?
      • Make sure that the Caps Lock key is not depressed. Login names are not case sensitive, but passwords are.
      • Make sure your browser is set to accept cookies.
  3. Biological Samples
    1. What kinds of samples does the database accept, and what attributes are stored?
    2. The database stores both nucleic acid preparations and constructed libraries. It tracks the sample's organism, the design intent (RNAseq, ChIPseq, etc.), protocol and crucial parameters, quality control details, tube identifier, concentration, and other important attributes. Generally, our specifications follow our genomics core's guidelines.

    3. How do I submit my sample(s) to the database?
    4. As of July 1, 2016, all samples and sequencing requests are typically entered through the Princeton University Core Facilities iLab Portal. The Core staff will transmit your samples and requests into HTSEQ.

      For those unrestricted researchers that construct their own complex libraries, and wish to track all the layers of sample provenance (sample protocols, sample multiplexing, library constructs, etc.), there are two sample submission interfaces:

      1. individual submission, via webform
      2. batch submission, via either webform or file upload

    5. How do I enter my custom multiplexed library into the database?
    6. We would recommend the following steps :

      1. enter the set of individual indexed libraries using the batch submission interface
      2. upon submission of those samples, there is a subsequent button to continue to pool those samples, which comprise the multiplexed library. This new record will have links back to the original indexed libraries.

  4. System questions
    1. How can I find out about the database schema?
    2. The schema definition is available from the database table specifications page.