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  1. IGB
  2. IGBF-3391

Create scaled and junction files for 2022 Palanivelu Lab-generated samples

        Details

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

          Description

          Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq

          • Rename "sorted" names
          • Create scaled coverage graphs
          • Create junction files

          Note: Remember to use 2019 and 2022 2bit files for SL4 and SL5. Also make sure to change find_junctions.sh to use that specific 2019 or 2022 2bit file.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3392 Make sample sheet for 2022 Palanivelu

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3390 Run Nextflow with 2022 Palanivelu Lab-generated samples

              • 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-3251 [ 22132 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3367 [ IGBF-3367 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3390 [ IGBF-3390 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3392 [ IGBF-3392 ]
                Mdavis4290 Molly Davis made changes -
                Summary Create scaled and junction files for 2022 Palanavelu Lab-generated samples Create scaled and junction files for 2022 Palanivelu Lab-generated samples
                Mdavis4290 Molly Davis made changes -
                Sprint Summer 5 2023 July 10 [ 174 ] Summer 6 2023 July 24 [ 175 ]
                Mdavis4290 Molly Davis made changes -
                Description Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq
                Nf-core run: /nobackup/tomato_genome/ravi-55/sl5-nfcore/results # but there are no scaled or junction files.

                * Rename "sorted" names
                * Create scaled coverage graphs
                * Create junction files

                		Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq
                Nf-core run: /nobackup/tomato_genome/ravi-55/sl5-nfcore/results # but there are no scaled or junction files.

                * Rename "sorted" names
                * Create scaled coverage graphs
                * Create junction files

                Note: Remember to use 2019 and 2022 2bit files for SL4 and SL5.
                Mdavis4290 Molly Davis made changes -
                Description Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq
                Nf-core run: /nobackup/tomato_genome/ravi-55/sl5-nfcore/results # but there are no scaled or junction files.

                * Rename "sorted" names
                * Create scaled coverage graphs
                * Create junction files

                Note: Remember to use 2019 and 2022 2bit files for SL4 and SL5.                 		Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq

                * Rename "sorted" names
                * Create scaled coverage graphs
                * Create junction files

                Note: Remember to use 2019 and 2022 2bit files for SL4 and SL5.
                Mdavis4290 Molly Davis made changes -
                Description Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq

                * Rename "sorted" names
                * Create scaled coverage graphs
                * Create junction files

                Note: Remember to use 2019 and 2022 2bit files for SL4 and SL5.                 		Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq

                * Rename "sorted" names
                * Create scaled coverage graphs
                * Create junction files

                Note: Remember to use 2019 and 2022 2bit files for SL4 and SL5. Also make sure to change find_junctions.sh to use that specific 2019 or 2022 2bit file.
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                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 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Robert Reid [ robertreid ] Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Robert Reid [ robertreid ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 6 2023 July 24 [ 175 ] Summer 6 2023 July 24, Summer 7 2023 Aug 7 [ 175, 176 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                robofjoy Robert Reid made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                robofjoy Robert Reid made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                robofjoy Robert Reid made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                robofjoy Robert Reid made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                robofjoy Robert Reid made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                robofjoy Robert Reid made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                robofjoy Robert Reid made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Robert Reid [ robertreid ] Molly Davis [ molly ]

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    Mdavis4290 Molly Davis
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: