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  1. IGB
  2. IGBF-3928

Shotgun assembly submission to the TSA

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Purpose: To submit the de novo assembled RNA-Seq contigs to NCBI's TSA archive.

          Since our raw reads already exist as a SRA, this should be straightforward. I just need to align reads to assemblies and the upload assemblies.

            Attachments

              Issue Links

              is blocked by

              Task - A task that needs to be done. IGBF-3944 Python script to remove NCBI's contaminants

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                robofjoy Robert Reid created issue -
                robofjoy Robert Reid made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                robofjoy Robert Reid made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                robofjoy Robert Reid made changes -
                Assignee Robert Reid [ robertreid ] Brandon Bendickson [ bbendick ]
                bbendick Brandon Bendickson made changes -
                Assignee Brandon Bendickson [ bbendick ] Robert Reid [ robertreid ]
                bbendick Brandon Bendickson made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 2 [ 203 ] Fall 2, Fall 3 [ 203, 204 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                robofjoy Robert Reid made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                robofjoy Robert Reid made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                robofjoy Robert Reid made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                bbendick Brandon Bendickson made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                robofjoy Robert Reid made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                robofjoy Robert Reid made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                robofjoy Robert Reid made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                robofjoy Robert Reid made changes -
                Link This issue is blocked by IGBF-3944 [ IGBF-3944 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 2, Fall 3 [ 203, 204 ] Fall 2, Fall 3, Fall 4 [ 203, 204, 205 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                robofjoy Robert Reid made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 2, Fall 3, Fall 4 [ 203, 204, 205 ] Fall 2, Fall 3, Fall 4, Fall 5 [ 203, 204, 205, 206 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                robofjoy Robert Reid made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                robofjoy Robert Reid made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                robofjoy Robert Reid made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                robofjoy Robert Reid made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                robofjoy Robert Reid made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                robofjoy Robert Reid made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                robofjoy Robert Reid made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                robofjoy Robert Reid made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                robofjoy Robert Reid made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                robofjoy Robert Reid made changes -
                Resolution Done [ 10000 ]
                Status Closed [ 6 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 2, Fall 3, Fall 4, Fall 5 [ 203, 204, 205, 206 ] Fall 2, Fall 3, Fall 4, Fall 5, Fall 6 [ 203, 204, 205, 206, 207 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                robofjoy Robert Reid made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                robofjoy Robert Reid made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                robofjoy Robert Reid made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                robofjoy Robert Reid made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                robofjoy Robert Reid made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                robofjoy Robert Reid made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                robofjoy Robert Reid made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                robofjoy Robert Reid made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                robofjoy Robert Reid made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                robofjoy Robert Reid made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                robofjoy Robert Reid made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                robofjoy Robert Reid made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                robofjoy Robert Reid made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    robofjoy Robert Reid
                    Reporter:
                    robofjoy Robert Reid
                  • Votes:
                    0 Vote for this issue
                    Watchers:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: