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  1. IGB
  2. IGBF-3250

Process muday-144 RNA-Seq data

        Details

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

          Description

          Rob has run nf-core rnaseq pipeline using SL4 and SL5 genome assemblies. Results are in: /nobackup/tomato_genome/muday-144/.

          For this task, complete RNA-Seq data processing:

          • Review QC file
          • Collect BAM files (removing "sorted" from the names)
          • Make scaled coverage graphs
          • Make junction files
          • Enter key data files into flavonoid-rnaseq repository - QC report, samples.csv used to run the pipeline, gene counts file, etc
          • Create sample description file for statistical analysis and Quickload metadata file generation
          • Deploy data files to Quickload for hosting

          Flavonoid RNA-Seq git repository: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/ (currently private)

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              relates to

              Task - A task that needs to be done. IGBF-3262 Make Markdown showing DESeq analysis of Muday time course SL5 data

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Description Rob has run nf-core rnaseq pipeline using SL4 and SL5 genome assemblies. Results are in: /nobackup/tomato_genome/muday-144/.

                For this task, complete RNA-Seq data processing:

                * Review QC file and attach to this ticket
                * Collect BAM files (removing "sorted" from the names)
                * Make scaled coverage graphs
                * Make junction files
                * Enter key data files into flavonoid-rnaseq repository
                * Create sample description file
                * Deploy data files to Quickload

                ann.loraine Ann Loraine made changes -
                Description Rob has run nf-core rnaseq pipeline using SL4 and SL5 genome assemblies. Results are in: /nobackup/tomato_genome/muday-144/.

                For this task, complete RNA-Seq data processing:

                * Review QC file and attach to this ticket
                * Collect BAM files (removing "sorted" from the names)
                * Make scaled coverage graphs
                * Make junction files
                * Enter key data files into flavonoid-rnaseq repository
                * Create sample description file
                * Deploy data files to Quickload

                		Rob has run nf-core rnaseq pipeline using SL4 and SL5 genome assemblies. Results are in: /nobackup/tomato_genome/muday-144/.

                For this task, complete RNA-Seq data processing:

                * Review QC file and attach to this ticket
                * Collect BAM files (removing "sorted" from the names)
                * Make scaled coverage graphs
                * Make junction files
                * Enter key data files into flavonoid-rnaseq repository - QC report, samples.csv used to run the pipeline, gene counts file, etc
                * Create sample description file for statistical analysis and Quickload metadata file generation
                * Deploy data files to Quickload

                ann.loraine Ann Loraine made changes -
                Description Rob has run nf-core rnaseq pipeline using SL4 and SL5 genome assemblies. Results are in: /nobackup/tomato_genome/muday-144/.

                For this task, complete RNA-Seq data processing:

                * Review QC file and attach to this ticket
                * Collect BAM files (removing "sorted" from the names)
                * Make scaled coverage graphs
                * Make junction files
                * Enter key data files into flavonoid-rnaseq repository - QC report, samples.csv used to run the pipeline, gene counts file, etc
                * Create sample description file for statistical analysis and Quickload metadata file generation
                * Deploy data files to Quickload

                		Rob has run nf-core rnaseq pipeline using SL4 and SL5 genome assemblies. Results are in: /nobackup/tomato_genome/muday-144/.

                For this task, complete RNA-Seq data processing:

                * Review QC file and attach to this ticket
                * Collect BAM files (removing "sorted" from the names)
                * Make scaled coverage graphs
                * Make junction files
                * Enter key data files into flavonoid-rnaseq repository - QC report, samples.csv used to run the pipeline, gene counts file, etc
                * Create sample description file for statistical analysis and Quickload metadata file generation
                * Deploy data files to Quickload for hosting

                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Summary Process Muday-144 RNA-Seq data Process muday-144 RNA-Seq data
                ann.loraine Ann Loraine made changes -
                Description Rob has run nf-core rnaseq pipeline using SL4 and SL5 genome assemblies. Results are in: /nobackup/tomato_genome/muday-144/.

                For this task, complete RNA-Seq data processing:

                * Review QC file and attach to this ticket
                * Collect BAM files (removing "sorted" from the names)
                * Make scaled coverage graphs
                * Make junction files
                * Enter key data files into flavonoid-rnaseq repository - QC report, samples.csv used to run the pipeline, gene counts file, etc
                * Create sample description file for statistical analysis and Quickload metadata file generation
                * Deploy data files to Quickload for hosting

                		Rob has run nf-core rnaseq pipeline using SL4 and SL5 genome assemblies. Results are in: /nobackup/tomato_genome/muday-144/.

                For this task, complete RNA-Seq data processing:

                * Review QC file and attach to this ticket
                * Collect BAM files (removing "sorted" from the names)
                * Make scaled coverage graphs
                * Make junction files
                * Enter key data files into flavonoid-rnaseq repository - QC report, samples.csv used to run the pipeline, gene counts file, etc
                * Create sample description file for statistical analysis and Quickload metadata file generation
                * Deploy data files to Quickload for hosting

                Flavonoid RNA-Seq git repository: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/ (currently private)
                ann.loraine Ann Loraine made changes -
                Description Rob has run nf-core rnaseq pipeline using SL4 and SL5 genome assemblies. Results are in: /nobackup/tomato_genome/muday-144/.

                For this task, complete RNA-Seq data processing:

                * Review QC file and attach to this ticket
                * Collect BAM files (removing "sorted" from the names)
                * Make scaled coverage graphs
                * Make junction files
                * Enter key data files into flavonoid-rnaseq repository - QC report, samples.csv used to run the pipeline, gene counts file, etc
                * Create sample description file for statistical analysis and Quickload metadata file generation
                * Deploy data files to Quickload for hosting

                Flavonoid RNA-Seq git repository: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/ (currently private)
                		Rob has run nf-core rnaseq pipeline using SL4 and SL5 genome assemblies. Results are in: /nobackup/tomato_genome/muday-144/.

                For this task, complete RNA-Seq data processing:

                * Review QC file
                * Collect BAM files (removing "sorted" from the names)
                * Make scaled coverage graphs
                * Make junction files
                * Enter key data files into flavonoid-rnaseq repository - QC report, samples.csv used to run the pipeline, gene counts file, etc
                * Create sample description file for statistical analysis and Quickload metadata file generation
                * Deploy data files to Quickload for hosting

                Flavonoid RNA-Seq git repository: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/ (currently private)
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                ann.loraine Ann Loraine made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Attachment Screen Shot 2023-02-08 at 4.19.38 PM.png [ 17675 ]
                Mdavis4290 Molly Davis made changes -
                Attachment muday22_multiqc_report.html [ 17676 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] 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 -
                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 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3262 [ IGBF-3262 ]

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: