Uploaded image for project: 'IGB'
  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)

            Attachments

              Issue Links

              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

                No work has yet been logged on this issue.

                  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: