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  1. IGB
  2. IGBF-3477

EBSEQ: The bigger table version

        Details

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

          Description

          The goal is to add to the existing EB-SEQ table results (From IBGF-3454).

          The table currently includes the EB-SEQ results along with the SolyID and gene description.

          What we can add:

          • The read expression counts data from Salmon.
          • The deseq2 results, values, log fold changes, pvalues, etc.
          • EdgeR data

          This would produce an unwieldy table, 100's of columns long!
          I am going to first touch base with Gloria about what would be the most useful.

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              is blocked by

              Task - A task that needs to be done. IGBF-3489 Tweaking the EBSEQ to merge results into a master table

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

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                robofjoy Robert Reid added a comment -

                Did not get to chat with Gloria in Wake Forest. She was juggling 50 things!

                What might look cool in this table would be the MvW results that Ann produced comparing are versus VF36 and recently shared with Gloria's lab.

                Table I refer to is in bitbucket here:
                https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/results/MvW-SL4.txt

                We have the following comparisons:

                awk '

                { print $2 "\t" $3 }

                ' MvW-SL4.txt | sort | uniq

                • A.28 V.28
                • V.28.15 A.28.15
                • V.28.30 A.28.30
                • V.28.45 A.28.45
                • V.28.75 A.28.75
                • V.34.15 A.34.15
                • V.34.30 A.34.30
                • V.34.45 A.34.45
                • V.34.75 A.34.75

                Each of these sets could be added as columns to the EBSEQ table. I am thinking of adding just the LOGFOLD change result for each set.
                Or maybe the P-value also. This would be 9 expts X 2 results for 18 more columns!

                Still manageable I think.
                Sounds like a Python script!

                Show
                robofjoy Robert Reid added a comment - Did not get to chat with Gloria in Wake Forest. She was juggling 50 things! What might look cool in this table would be the MvW results that Ann produced comparing are versus VF36 and recently shared with Gloria's lab. Table I refer to is in bitbucket here: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/results/MvW-SL4.txt We have the following comparisons: awk ' { print $2 "\t" $3 } ' MvW-SL4.txt | sort | uniq A.28 V.28 V.28.15 A.28.15 V.28.30 A.28.30 V.28.45 A.28.45 V.28.75 A.28.75 V.34.15 A.34.15 V.34.30 A.34.30 V.34.45 A.34.45 V.34.75 A.34.75 Each of these sets could be added as columns to the EBSEQ table. I am thinking of adding just the LOGFOLD change result for each set. Or maybe the P-value also. This would be 9 expts X 2 results for 18 more columns! Still manageable I think. Sounds like a Python script!
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                robofjoy Robert Reid added a comment -

                Until we hear back from Gloria's group that they plan to harness this analysis in some way, we will close this task.

                When they ask for this again along with more related data, we can open a new ticket at that time.

                Show
                robofjoy Robert Reid added a comment - Until we hear back from Gloria's group that they plan to harness this analysis in some way, we will close this task. When they ask for this again along with more related data, we can open a new ticket at that time.

                  People

                  • Assignee:
                    robofjoy Robert Reid
                    Reporter:
                    robofjoy Robert Reid
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                    • Created:
                      Updated:
                      Resolved: