Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-3758

Trinity NEXTFLOW alignment

        Details

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

          Description

          GOAL:

          To use the newly annotated Trinity files as a REFERENCE to align reads to and determine gene expression for Kelsey's dataset.

          There are 4 newly generated Trinity sets of contigs (TMNH). See IGBF-3741.

          Want to run NEXTFLOW. One for each variety.

          Location of Trinity COntigs:
          /projects/tomato_genome/fnb/dataprocessing/trinity/NEXTFLOW/postblat
          (there should be 4 fasta files here, if not yet, soon.....)

          The reads that will be used are here:
          /projects/tomato_genome/rnaseq/renamed_Ravi_Combined

          Instead of running ALL reads, we be separating by variety.
          So only using the reads fr heinz with the Heinz trinity contig file......

            Attachments

              Activity

                People

                • Assignee:
                  robofjoy Robert Reid
                  Reporter:
                  robofjoy Robert Reid
                • Votes:
                  0 Vote for this issue
                  Watchers:
                  1 Start watching this issue

                  Dates

                  • Created:
                    Updated:
                    Resolved: