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  1. IGB
  2. IGBF-3817

Create a method to compare NextFlow gene expression results

        Details

        • Type: Task
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          GOAL: To compare our results generated by De novo assemblies to the standard reference based strategies to see if there is indeed bias with Heinz.

          This is the final big step in this somewhat tedious pipeline.

          This can't be done until ticket 3772 is satisfied. Need the actual Nextflow gene counts.

          We can then do a simple gene count comparison (for every gene!).
          Make a big table, each row are the Soly genes. Columns are the 4 varieties done both de novo and refrerence based. Calculate which ones that differ by 25% maybe? (or 10% ?)

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              is blocked by

              Task - A task that needs to be done. IGBF-3843 Free up space for tomato genome on the URC

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3772 Run NEXTFLOW on contigs that are NOT SL4 or SL5

              • Minor - Minor loss of function, or other problem where easy workaround is present.
              • Closed

                Activity

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                robofjoy Robert Reid created issue -
                robofjoy Robert Reid made changes -
                Field Original Value New Value
                Link This issue is blocked by IGBF-3772 [ IGBF-3772 ]
                robofjoy Robert Reid made changes -
                Sprint Summer 5 [ 199 ]
                nfreese Nowlan Freese made changes -
                Epic Link IGBF-2993 [ 21429 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 5 [ 199 ] Summer 5, Summer 6 [ 199, 200 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                robofjoy Robert Reid made changes -
                Link This issue is blocked by IGBF-3843 [ IGBF-3843 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 5, Summer 6 [ 199, 200 ] Summer 5, Summer 6, Summer 7 [ 199, 200, 201 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Story Points 2 4
                ann.loraine Ann Loraine made changes -
                Sprint Summer 5, Summer 6, Summer 7 [ 199, 200, 201 ] Summer 5, Summer 6, Summer 7, Fall 1 [ 199, 200, 201, 202 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                robofjoy Robert Reid made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 5, Summer 6, Summer 7, Fall 1 [ 199, 200, 201, 202 ] Summer 5, Summer 6, Summer 7, Fall 1, Fall 2 [ 199, 200, 201, 202, 203 ]
                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 Summer 5, Summer 6, Summer 7, Fall 1, Fall 2 [ 199, 200, 201, 202, 203 ] Summer 5, Summer 6, Summer 7, Fall 1, Fall 2, Fall 3 [ 199, 200, 201, 202, 203, 204 ]
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
                Sprint Summer 5, Summer 6, Summer 7, Fall 1, Fall 2, Fall 3 [ 199, 200, 201, 202, 203, 204 ] Summer 5, Summer 6, Summer 7, Fall 1, Fall 2, Fall 3, Fall 4 [ 199, 200, 201, 202, 203, 204, 205 ]
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
                Sprint Summer 5, Summer 6, Summer 7, Fall 1, Fall 2, Fall 3, Fall 4 [ 199, 200, 201, 202, 203, 204, 205 ] Summer 5, Summer 6, Summer 7, Fall 1, Fall 2, Fall 3, Fall 4, Fall 5 [ 199, 200, 201, 202, 203, 204, 205, 206 ]
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine added a comment -

                Robert Reid: I am removing this from our sprints since it looks like we won't be able to do this task yet. It will of course stay available in the epic and can be moved back into a sprint whenever we are ready to get started on it. If you would like it to be in a sprint again, please feel free to add it back at your convenience!

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                ann.loraine Ann Loraine added a comment - Robert Reid : I am removing this from our sprints since it looks like we won't be able to do this task yet. It will of course stay available in the epic and can be moved back into a sprint whenever we are ready to get started on it. If you would like it to be in a sprint again, please feel free to add it back at your convenience!
                ann.loraine Ann Loraine made changes -
                Sprint Summer 5, Summer 6, Summer 7, Fall 1, Fall 2, Fall 3, Fall 4, Fall 5 [ 199, 200, 201, 202, 203, 204, 205, 206 ] Summer 5, Summer 6, Summer 7, Fall 1, Fall 2, Fall 3, Fall 4 [ 199, 200, 201, 202, 203, 204, 205 ]

                  People

                  • Assignee:
                    robofjoy Robert Reid
                    Reporter:
                    robofjoy Robert Reid
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                    Dates

                    • Created:
                      Updated: