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  1. IGB
  2. IGBF-3424

Re-run mature pollen and seedling pipeline with SL5 using data newly submitted to SRA

        Details

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

          Description

          SRP438952

          For this task, we need to confirm and sanity-check the seedling and mature pollen data that Rob recently 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.

            Attachments

              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-3544 Re-run mature pollen and seedling pipeline with SL4 using data newly submitted to SRA

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                Mdavis4290 Molly Davis created issue -
                Mdavis4290 Molly Davis made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                Mdavis4290 Molly Davis made changes -
                Description SRP438952

                For this task, we need to confirm and sanity-check the seedling and mature pollen data that Rob recently 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:
                Download the data onto the cluster
                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.                 		SRP438952

                For this task, we need to confirm and sanity-check the seedling and mature pollen data that Rob recently 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
                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.
                Mdavis4290 Molly Davis made changes -
                Description SRP438952

                For this task, we need to confirm and sanity-check the seedling and mature pollen data that Rob recently 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
                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.                 		SRP438952

                For this task, we need to confirm and sanity-check the seedling and mature pollen data that Rob recently 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
                * 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.
                Mdavis4290 Molly Davis made changes -
                Description SRP438952

                For this task, we need to confirm and sanity-check the seedling and mature pollen data that Rob recently 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
                * 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.                 		SRP438952

                For this task, we need to confirm and sanity-check the seedling and mature pollen data that Rob recently 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
                * 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.
                Mdavis4290 Molly Davis made changes -
                Description SRP438952

                For this task, we need to confirm and sanity-check the seedling and mature pollen data that Rob recently 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
                * 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.                 		SRP438952

                For this task, we need to confirm and sanity-check the seedling and mature pollen data that Rob recently 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.
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 8 2023 Aug 21 [ 177 ] Testing 2 : 4 Nov - 15 Nov, Summer 8 2023 Aug 21 [ 82, 177 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                robofjoy Robert Reid made changes -
                Assignee Robert Reid [ robertreid ]
                robofjoy Robert Reid made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                robofjoy Robert Reid made changes -
                Assignee Robert Reid [ robertreid ] Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Comment [ *Branch*: https://bitbucket.org/mdavis4290/molly-splicing-analysis/branch/IGBF-3424

                Includes:
                * MultiQC Report
                * CSV

                [~aloraine] ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                Mdavis4290 Molly Davis made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                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 -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                Mdavis4290 Molly Davis 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 Ann Loraine [ aloraine ] Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3498 [ IGBF-3498 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3499 [ IGBF-3499 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3512 [ IGBF-3512 ]
                Mdavis4290 Molly Davis made changes -
                Summary Re-run mature pollen and seedling pipeline using data newly submitted to SRA Re-run mature pollen and seedling pipeline with SL5 using data newly submitted to SRA
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3544 [ IGBF-3544 ]

                  People

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

                    • Created:
                      Updated:
                      Resolved: