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  1. IGB
  2. IGBF-3406

Re-run Nextflow Muday time course data with SL5 data downloaded from SRA

        Details

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

          Description

          Refer to ticket IGBF-3423 to locate SRA data.

          SRP460750

          For this task, we need to confirm and sanity-check the Muday time course data that Rob uploaded and submitted to the Sequence Read Archive.
          If the data are good, we will replace all the existing BAM, junctions, etc. files deployed in the "hotpollen" quickload site with newly processed data.
          For this task:

          • Check SRP on NCBI and review submission
          • Download the data onto the cluster by using the SRP name
          • Run nf-core/rnaseq pipeline
          • Run our coverage graph and junctions scripts on the data

          Note that all files should now use their "SRR" names instead of the existing file names.

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              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3498 Review SRA Submissions

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3499 Complete evaluation of RNA-Seq dataset submissions

              • Major - Major loss of function.
              • Closed

              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-3507 Re-run Nextflow Muday time course data with SL4 and data downloaded from SRA

              • 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

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                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    Mdavis4290 Molly Davis
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                    • Created:
                      Updated:
                      Resolved: