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  1. IGB
  2. IGBF-3323

Generate scaled coverage graphs Kelsey's Palanivelu Lab 2023

        Details

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

          Description

          RR has downloaded the data onto the UNCC cluster and saved it here: /projects/tomato_genome/rnaseq/30-804059537-kelsie.
          Please do the data processing in this directory:
          /nobackup/tomato_genome/30-804059537-KP (kp for "Kelsey Pryze")
          Bitbucket repo: https://bitbucket.org/hotpollen/pistil-rna-seq

          Already ran pipeline IGBF-3251.

          Next Steps:

          • Generate scaled coverage graphs (Molly)

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3325 Copy KP 2023 data (30-804059537) to IGB Quickload host for visualization in IGB

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3326 Create KP 2023 sample sheet needed for Quickload site and more

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3324 Generate junction files Kelsey's Palanivelu Lab 2023

              • Major - Major loss of function.
              • Closed

                Activity

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                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 -
                Rank Ranked higher
                Mdavis4290 Molly Davis made changes -
                Link This issue is blocked by IGBF-3324 [ IGBF-3324 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue is blocked by IGBF-3325 [ IGBF-3325 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue is blocked by IGBF-3326 [ IGBF-3326 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
                Permalink
                Mdavis4290 Molly Davis added a comment - - edited

                Scaled Coverage Graphs Directory: /nobackup/tomato_genome/30-804059537-KP/results/star_salmon

                Files used:

                • renameBams.sh
                • bamCoverage.sh
                • sbatch-doIt.sh

                Should I add these files to bitbucket 'src'? https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/src/main/src/

                Show
                Mdavis4290 Molly Davis added a comment - - edited Scaled Coverage Graphs Directory : /nobackup/tomato_genome/30-804059537-KP/results/star_salmon Files used: renameBams.sh bamCoverage.sh sbatch-doIt.sh Should I add these files to bitbucket 'src'? https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/src/main/src/
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3324 [ IGBF-3324 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue is blocked by IGBF-3324 [ IGBF-3324 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue is blocked by IGBF-3325 [ IGBF-3325 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue is blocked by IGBF-3326 [ IGBF-3326 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3325 [ IGBF-3325 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3326 [ IGBF-3326 ]
                Mdavis4290 Molly Davis made changes -
                Comment [ Also where should I add multiqc report and CSV file in bitbucket repo? ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
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                ann.loraine Ann Loraine added a comment -

                Coverage graphs exist in /nobackup/tomato_genome/30-804059537-KP/results/star_salmon.
                Moving to DONE.

                Answering Molly's question: I will add them.

                Show
                ann.loraine Ann Loraine added a comment - Coverage graphs exist in /nobackup/tomato_genome/30-804059537-KP/results/star_salmon. Moving to DONE. Answering Molly's question: I will add them.
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Scripts are added to the team repository bitbucket.org/hotpollen/pistil-rna-seq

                Show
                ann.loraine Ann Loraine added a comment - Scripts are added to the team repository bitbucket.org/hotpollen/pistil-rna-seq
                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 Ann Loraine [ aloraine ] Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Summary Generate scaled coverage graphs Kelsey's Palanivelu Lab Generate scaled coverage graphs Kelsey's Palanivelu Lab 2023

                  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: