Uploaded image for project: 'UGENE'
  1. UGENE
  2. UGENE-453

Support assembly coverage formats

    XMLWordPrintable

    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 1.15
    • Component/s: None
    • Tests Type:
      GUI automatic
    • Sprint:
      DEV-11/09/2016, DEV-18/09/2014, DEV-25/09/2014, DEV-02/10/2014, DEV-16/10/2014, DEV-23/10/2014, DEV-06/11/2014, DEV-13/11/2014, DEV-20/11/2014, DEV-18/12/2014
    • Affect Type:
      Userdefined

      Description

      Assembly coverage information can be stored in well-known formats: pileup, TDF, wig: http://genomeview.org/manual/Preparing_value_data (old link: http://genomeview.org/content/preparing-pileup)
      We have to support such formats for import/export. There should be a possibility to work with zipped files. An optional threshold value should be introduced, regions that don't match this value should be skipped.

      Information to export (if the output file format supports it):
      coverage (quantity reads per position)
      quantity of every symbol per position (optional)

      A workflow designer worker and a sample is to be added.

        Attachments

          Issue Links

            Activity

              People

              Assignee:
              atiunov Aleksey Tiunov [X] (Inactive)
              Reporter:
              iefremov Ivan Efremov
              Assigned Tester:
              German Grekhov
              Watchers:
              3 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved:

                  Time Tracking

                  Estimated:
                  Original Estimate - 2 days
                  2d
                  Remaining:
                  Remaining Estimate - 1 hour
                  1h
                  Logged:
                  Time Spent - Not Specified Time Not Required
                  Not Specified