Not logged in
  • Log in
    Membership (41444+) Group hosting [?] Wiki
    Franklin Award

    About bioinformatics
    Bioinformatics training
    Bioinformatics jobs

    All information groups
    Online databases Online analysis tools Online education tools More tools

    All software groups
    FTP repository
    SVN & CVS repositories [?]
    Mailing lists

    News & Commentary
  • Submit
  • Archives
  • Subscribe

  • Jobs Forum
    (Career Center)
  • Submit
  • Archives
  • Subscribe
  • CATCH - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #705 ] import Barski wigfiles, only one track is loaded to graphs
    01/09/09 04:20
    Submitted by:
    Assigned to:
    ALG file handling
    Ticket group:
    import Barski wigfiles, only one track is loaded to graphs
    Original submission:
    - Load multiple wigfiles (varstep) from the Barski ChIP-seq data
    - Load a bedfile
    - 'Convert and add to CATCH'

    Three pwig files are generated, but only one track is shown in the graphs view.
    No exceptions or error messages are shown.

    Update Jan 9, 2009 by glyn_dk:
    I have located the error. In the the Barski wigfiles the tracks do not have signal values for all positions. Since profiles of less than two signal values are ignored, the pwig files may contain different numbers of profiles.
    When adding pwigs to dataset files that do not have the correct number of profiles are ignored. I have added an error message to this special case: "ERROR: mismatch in number of profiles in selected tracks"

    In general it should be possible for the user to use these tracks together, so we have to construct a workaround.

    Suggestion for workaround:
    - the generation of the pwig files shall remain the same
    - the user can choose either of two options when loading data: 1) discard profiles with no signal values defined 2) pad with zeros in tracks where no signal values are defined.
    Please log in to add comments and receive followups via email.
    Comment Date By
    Implemented workaround:
    - pwig files now include a profile name ( e.g. # chr2:220006943-220008943) for all selected positions, regardless of whether the selected region has signal values defined within it.
    - when readSequences reads a sequence (a profile region) with less than two signals defined, two dummy signals are inserted with value 0.
    - the interpolation of the zero values gives a track with zero signal at all reference positions.

    Now users can define any crazy region or load tracks with lots of missing data (e.g. ChIP-seq tracks) without encountering an error message or runtime exception.
    01/11/09 07:24 glyn_dk
    HIGH PRIORITY: Must be fixed before next release! 01/09/09 04:22 glyn_dk
    No results for "Dependent on ticket"
    No results for "Dependent on Task"
    No other tickets are dependent on this ticket
    Ticket change history
    Field Old value Date By
    status_id Unset 01/11/09 07:24 glyn_dk
    assigned_to unset 01/11/09 07:24 glyn_dk
    resolution_id Unset 01/11/09 07:24 glyn_dk
    close_date 12/31/69 19:00 01/11/09 07:24 glyn_dk
    priority 5 01/09/09 04:22 glyn_dk


    Copyright © 2019 · Scilico, LLC