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  1. IGB
  2. IGBF-3499

Complete evaluation of RNA-Seq dataset submissions

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          2
        • Epic Link:
        • Sprint:
          Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4, Summer 5, Summer 6, Summer 7, Fall 1

          Description

          Directory: /projects/tomato_genome/fnb/dataprocessing
          Review the SRA re-runs on the cluster for Muday, Johnson, mature pollen, and Ravi lab data. Once bam, junction, and coverage graph files have been produced and checked deploy data to IGB Quickload hotpollen host.

          NOTE: This ticket changed in scope and focus a bit! The new goal is:

          • Complete comparative evaluation of pre- and post-submission RNA-Seq data using multiqc results and special code written for this purpose.

          This goal builds on the final work that Molly Davis did for us, before her appointment ended. We need to complete this work this sprint because we need to recover the large amount of disk space used up by running nf-core/rnaseq pipeline.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3500 Re-run mark-2022-timeseries data with data downloaded from SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3544 Re-run mature pollen and seedling pipeline with SL4 using data newly submitted to SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3545 Re-run nextflow Mark pollen tube data for SL4 and SL5 with data dowloaded from SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3589 Re-run nextflow Ravi 30-681594536 data for SL4 and SL5 with data dowloaded from SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3590 Re-run nextflow Ravi 30-804059537 data for SL4 and SL5 with data dowloaded from SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3591 Re-run nextflow Ravi 30-605730043 data for SL4 and SL5 with data dowloaded from SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3406 Re-run Nextflow Muday time course data with SL5 data downloaded from SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3424 Re-run mature pollen and seedling pipeline with SL5 using data newly submitted to SRA

              • Major - Major loss of function.
              • Closed

                Activity

                  People

                  • Assignee:
                    bbendick Brandon Bendickson
                    Reporter:
                    Mdavis4290 Molly Davis
                  • Votes:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: