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  1. IGB
  2. IGBF-3290

Use new sample labels recommended by Muday Lab

        Details

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

          Description

          See attached.

          For this task, modify AddGeneAnnotations.Rmd to change labels as advised.

          A.34.15.8 is actually F.34.15.8 and vice versa
          A.28.30.8 is actually V.28.30.8 and vice versa
          A.34.45.8 is actually F.34.45.8 and vice versa
          A.28.75.8 is actually V.28.75.8 and vice versa

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              relates to

              Task - A task that needs to be done. IGBF-3303 Investigate: Distinguish F3H-OX3 from VF36 samples

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3333 Notify Muday lab about relabeled samples

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3596 Compare original Muday flavonoid data to SRA Re-run data

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3346 Prepping data and entries for SRA for Muday time course

              • Major - Major loss of function.
              • To-Do

                Activity

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                7 older comments
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                aloraine Ann Loraine added a comment - - edited

                Updated AddGeneAnnotations.Rmd to incorporate NEW sample renaming scheme recommended by Muday lab in

                • flavonoid-rnaseq/72_F3H_PollenTube/Documentation/Muday-lab-RNA-samples-for-sample-name-conversion.xlsx

                To review:

                • Read the knitted Markdowns AddGeneAnnotations.pdf and MakeMdsPlots.pdf
                • Check output file sample_renaming_summary.txt. Compare to Muday-lab-RNA-samples-for-sample-name-conversion.xlsx.

                Note that the new code and new files are already committed to the main branch of the team repository.

                Show
                aloraine Ann Loraine added a comment - - edited Updated AddGeneAnnotations.Rmd to incorporate NEW sample renaming scheme recommended by Muday lab in flavonoid-rnaseq/72_F3H_PollenTube/Documentation/Muday-lab-RNA-samples-for-sample-name-conversion.xlsx To review: Read the knitted Markdowns AddGeneAnnotations.pdf and MakeMdsPlots.pdf Check output file sample_renaming_summary.txt. Compare to Muday-lab-RNA-samples-for-sample-name-conversion.xlsx. Note that the new code and new files are already committed to the main branch of the team repository.
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                Mdavis4290 Molly Davis (Inactive) added a comment - - edited

                Gene annotations and Mds plots look like they have accurate renaming for samples provided by Muday lab. I compared the renaming summary to the naming conversions and they seem to match each other. Let me know if you would like to make a new ticket to perform the DESeq analysis with the new renamed counts file muday-144-SL5_counts-salmon.txt.

                Ann Loraine

                Show
                Mdavis4290 Molly Davis (Inactive) added a comment - - edited Gene annotations and Mds plots look like they have accurate renaming for samples provided by Muday lab. I compared the renaming summary to the naming conversions and they seem to match each other. Let me know if you would like to make a new ticket to perform the DESeq analysis with the new renamed counts file muday-144-SL5_counts-salmon.txt. Ann Loraine
                Hide
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                aloraine Ann Loraine added a comment - - edited

                No, instead make a ticket tracking notifying Muday Lab of the good news.

                Show
                aloraine Ann Loraine added a comment - - edited No, instead make a ticket tracking notifying Muday Lab of the good news.
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                aloraine Ann Loraine added a comment -

                Updating makeAnnotsXml.py to use the new labels.

                Show
                aloraine Ann Loraine added a comment - Updating makeAnnotsXml.py to use the new labels.
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                aloraine Ann Loraine added a comment -

                Committed new annots.xml file and new script version to repository

                Show
                aloraine Ann Loraine added a comment - Committed new annots.xml file and new script version to repository

                  People

                  • Assignee:
                    aloraine Ann Loraine
                    Reporter:
                    aloraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: