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  1. IGB
  2. IGBF-3740

Reorganize the Muday Lab folder in the RNA-Seq Quickload

        Details

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

          Description

          Situation: The RNA-Seq Quickload needs reorganizing prior to the ASPB workshop. Specifically, the Muday Lab folder is currently organized in a way that makes sense, but I think that we could optimize this folder for the workshop by organizing it a bit differently.

          Tasks:
          1. Reorganize the Muday Lab folder:

          • List all of the A (are) samples first, then V (VF36), then F (VF36-F3H-T3).
          • Within each of these subgroups, keep them listed in order first by time point, then by temperature, then by replicate.
          • Do this for all three subfolders (Reads, Coverage Graphs, and Junctions).

          2. Give the last folder in the tomato RNA-Seq Quickload ("SRP328042 - anther development under simulated drought stress") a name that matches with the other folders. I believe the PI associated with that SRP data is Gang Lu. Here's a link to their paper: https://www.mdpi.com/2073-4409/10/7/1809.

          With all of this information, the title of the folder after renaming should be something like "Lu Lab - anther, # varieties, drought stress, # minutes (SRP328042)".

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              Task - A task that needs to be done. IGBF-3672 Draft a workshop outline for ASPB 2024

              • Major - Major loss of function.
              • Closed

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                pkulzer Paige Kulzer created issue -
                pkulzer Paige Kulzer made changes -
                Field Original Value New Value
                Epic Link IGBF-2809 [ 19325 ]
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3672 [ IGBF-3672 ]
                pkulzer Paige Kulzer made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 10 [ 194 ] Spring 10, Summer 1 [ 194, 195 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
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                ann.loraine Ann Loraine added a comment - - edited

                I have made many changes to the organization and naming schemes for the data in IGB RNA-Seq quickload.
                First main change is that I sorted the "are" data from the Muday Lab as requested.
                Second main change is that all the data sets created for the NSF project - including data harvested from the SRA - now reside in a folder named for the project, with subfolders named for individual laboratories and tissue types investigated.
                I did this because I felt it is useful to separate different lab's datasets into folders because where a dataset was produced (the laboratory location) is a confounder in data analysis.
                Similarly, some experiments were done at different times, by different people. Those datasets are also separated into folders.
                Thus, I am separating data collections into folders using confounders. The idea is to make it super clear to users which collections of samples can be compared to each others in the same collection using standard methods, and which would need to be compared with the known confounders taken into account.

                Please review by visiting tomato genome assemblies from June 2022 (SL5) and Sept. 2019 (SL4).

                Show
                ann.loraine Ann Loraine added a comment - - edited I have made many changes to the organization and naming schemes for the data in IGB RNA-Seq quickload. First main change is that I sorted the "are" data from the Muday Lab as requested. Second main change is that all the data sets created for the NSF project - including data harvested from the SRA - now reside in a folder named for the project, with subfolders named for individual laboratories and tissue types investigated. I did this because I felt it is useful to separate different lab's datasets into folders because where a dataset was produced (the laboratory location) is a confounder in data analysis. Similarly, some experiments were done at different times, by different people. Those datasets are also separated into folders. Thus, I am separating data collections into folders using confounders. The idea is to make it super clear to users which collections of samples can be compared to each others in the same collection using standard methods, and which would need to be compared with the known confounders taken into account. Please review by visiting tomato genome assemblies from June 2022 (SL5) and Sept. 2019 (SL4).
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Paige Kulzer [ pkulzer ]
                pkulzer Paige Kulzer made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                pkulzer Paige Kulzer made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                pkulzer Paige Kulzer made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 10, Summer 1 [ 194, 195 ] Spring 10, Summer 1, Summer 2 [ 194, 195, 196 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                Hide
                Permalink
                pkulzer Paige Kulzer added a comment -

                The Muday lab folder is now organized well for the upcoming ASPB workshop. I noticed several things that I'd like to make note of, but these don't need to be fixed right now:

                • Some folders have SRP numbers, some have a longer string of numbers, and others have no number attached to them at all.
                • Similarly, folder names follow slightly different patterns. For example, some names follow the pattern, "[part of tomato] heat stress, [#] varieties, [time] min". Others follow a different pattern like "heat stress [time] min".
                • Some file names begin with a sample code (e.g., Muday > Reads), whereas others end with this sample code (e.g., Johnson Lab > 30 - 120 min timeseries > Reads)
                • File names from the Reproduction-related data... > Reads folder have SRR numbers, but no other file names in the Quickload have them.

                Thank you for these changes! Moving this ticket to done now that the Muday lab folder has been reorganized.

                Show
                pkulzer Paige Kulzer added a comment - The Muday lab folder is now organized well for the upcoming ASPB workshop. I noticed several things that I'd like to make note of, but these don't need to be fixed right now: Some folders have SRP numbers, some have a longer string of numbers, and others have no number attached to them at all. Similarly, folder names follow slightly different patterns. For example, some names follow the pattern, " [part of tomato] heat stress, [#] varieties, [time] min". Others follow a different pattern like "heat stress [time] min". Some file names begin with a sample code (e.g., Muday > Reads), whereas others end with this sample code (e.g., Johnson Lab > 30 - 120 min timeseries > Reads) File names from the Reproduction-related data... > Reads folder have SRR numbers, but no other file names in the Quickload have them. Thank you for these changes! Moving this ticket to done now that the Muday lab folder has been reorganized.
                pkulzer Paige Kulzer made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                pkulzer Paige Kulzer made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                pkulzer Paige Kulzer made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                pkulzer Paige Kulzer made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                pkulzer Paige Kulzer made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                pkulzer Paige Kulzer made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    pkulzer Paige Kulzer
                    Reporter:
                    pkulzer Paige Kulzer
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                      Updated:
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