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  1. IGB
  2. IGBF-3324

Generate junction files Kelsey's Palanivelu Lab 2023

        Details

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

          Description

          Directory: /nobackup/tomato_genome/30-804059537-KP (kp for "Kelsey Pryze")

          See IGBF-3165 for instructions.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3323 Generate scaled coverage graphs Kelsey's Palanivelu Lab 2023

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3325 Copy KP 2023 data (30-804059537) to IGB Quickload host for visualization in IGB

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3326 Create KP 2023 sample sheet needed for Quickload site and more

              • Major - Major loss of function.
              • Closed

                Activity

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                Mdavis4290 Molly Davis created issue -
                Mdavis4290 Molly Davis made changes -
                Field Original Value New Value
                Epic Link IGBF-3251 [ 22132 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue blocks IGBF-3323 [ IGBF-3323 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Link This issue is blocked by IGBF-3325 [ IGBF-3325 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue is blocked by IGBF-3326 [ IGBF-3326 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Description Directory: /nobackup/tomato_genome/30-804059537-KP (kp for "Kelsey Pryze") Directory: /nobackup/tomato_genome/30-804059537-KP (kp for "Kelsey Pryze")

                See IGBF-3165 for instructions.
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3323 [ IGBF-3323 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue blocks IGBF-3323 [ IGBF-3323 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue is blocked by IGBF-3325 [ IGBF-3325 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue is blocked by IGBF-3326 [ IGBF-3326 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3325 [ IGBF-3325 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3326 [ IGBF-3326 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
                Permalink
                Mdavis4290 Molly Davis added a comment - - edited

                Files needed in directory: /nobackup/tomato_genome/30-804059537-KP/results/star_salmon

                • S_lycopersicum_Jun_2022.2bit
                • find_junctions.sh
                • sbatch-doIt.sh
                • find-junctions-1.0.0-jar-with-dependencies.jar

                Notes: Made sure "find_junctions.sh" file referenced "S_lycopersicum_Jun_2022.2bit". 

                ./sbatch-doIt.sh .bam find_junctions.sh >jobs.out 2>jobs.err

                Review:

                Show
                Mdavis4290 Molly Davis added a comment - - edited Files needed in directory : /nobackup/tomato_genome/30-804059537-KP/results/star_salmon S_lycopersicum_Jun_2022.2bit find_junctions.sh sbatch-doIt.sh find-junctions-1.0.0-jar-with-dependencies.jar Notes: Made sure "find_junctions.sh" file referenced "S_lycopersicum_Jun_2022.2bit". ./sbatch-doIt.sh .bam find_junctions.sh >jobs.out 2>jobs.err Review: Can you access files? Do the files properly work? Should I add required scripts to bitbucket 'src'? https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/src/main/src/
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                I have added the scripts to the team repository.
                Moving to DONE.

                Show
                ann.loraine Ann Loraine added a comment - I have added the scripts to the team repository. Moving to DONE.
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Summary Generate junction files Kelsey's Palanivelu Lab Generate junction files Kelsey's Palanivelu Lab 2023

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    Mdavis4290 Molly Davis
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                    Dates

                    • Created:
                      Updated:
                      Resolved: