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  1. IGB
  2. IGBF-3239

Create scaled coverage graphs for SRP100604 and SRP268884

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          1
        • Epic Link:
        • Sprint:
          Spring 1 2023 Dec 26, Spring 2 2023 Jan 16, Spring 3 2023 Feb 1, Spring 4 2023 Feb 21

          Description

          For this task, create scaled coverage graphs for SRP100604 and SRP268884.

          See linked issue IGBF-3162 for scripts used previously.

            Attachments

              Issue Links

              is blocked by

              Task - A task that needs to be done. IGBF-3228 Download and process data for SRP100604 and SRP268884

              • Major - Major loss of function.
              • Closed
              relates to

              Task - A task that needs to be done. IGBF-3162 Generate scaled coverage graphs for RNA-Seq alignments

              • Major - Major loss of function.
              • Closed

                Activity

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                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 -
                Link This issue relates to IGBF-3228 [ IGBF-3228 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3162 [ IGBF-3162 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3228 [ IGBF-3228 ]
                ann.loraine Ann Loraine made changes -
                Link This issue is blocked by IGBF-3228 [ IGBF-3228 ]
                ann.loraine Ann Loraine made changes -
                Description For this task, create scaled coverage graphs for SRP100604 and SRP268884.

                		For this task, create scaled coverage graphs for SRP100604 and SRP268884.

                See linked issue IGBF-3162 for scripts used previously.
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Hide
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                Mdavis4290 Molly Davis added a comment - - edited

                Notes: Made sure no bam files contained the word 'sorted' in file name. Added bamCoverage.sh and sbatch-doIt.sh scripts to SRP100604 & SRP268884 directories where bam files are located. 

                /nobackup/tomato_genome/alt_splicing/SRP100604/results/star_salmon

                /nobackup/tomato_genome/alt_splicing/SRP268884/results/star_salmon

                Launched Jobs with: 

                sbatch-doIt.sh .bam bamCoverage.sh >jobs.out 2>jobs.err

                Error: -bash: sbatch-doIt.sh: command not found

                Fixed error with: 

                ./sbatch-doIt.sh .bam bamCoverage.sh >jobs.out 2>jobs.err

                Moved files to Directories: 

                /nobackup/tomato_genome/alt_splicing/for_igbquickload/coverage_graphs_2/coverage_graphs_SRP100604

                /nobackup/tomato_genome/alt_splicing/for_igbquickload/coverage_graphs_2/coverage_graphs_SRP268884
                Show
                Mdavis4290 Molly Davis added a comment - - edited Notes: Made sure no bam files contained the word 'sorted' in file name. Added bamCoverage.sh and sbatch-doIt.sh scripts to SRP100604 & SRP268884 directories where bam files are located. /nobackup/tomato_genome/alt_splicing/SRP100604/results/star_salmon /nobackup/tomato_genome/alt_splicing/SRP268884/results/star_salmon Scripts: https://bitbucket.org/hotpollen/splicing-analysis/src/main/src/ Made execute permissions on cluster for scripts with: chmod +x sbatch-doIt.sh chmod +x bamCoverage.sh Launched Jobs with: sbatch-doIt.sh .bam bamCoverage.sh >jobs.out 2>jobs.err Error : -bash: sbatch-doIt.sh: command not found Fixed error with : ./sbatch-doIt.sh .bam bamCoverage.sh >jobs.out 2>jobs.err Moved files to Directories: /nobackup/tomato_genome/alt_splicing/for_igbquickload/coverage_graphs_2/coverage_graphs_SRP100604 /nobackup/tomato_genome/alt_splicing/for_igbquickload/coverage_graphs_2/coverage_graphs_SRP268884
                ann.loraine Ann Loraine made changes -
                Sprint Spring 1 2023 Dec 26 [ 161 ] Spring 1 2023 Dec 26, Spring 2 2023 Jan 16 [ 161, 162 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
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                ann.loraine Ann Loraine added a comment -

                if the current working directory is not in your PATH, you need to specify the directory when you run the script, e.g., 

                ./sbatch-doIt.sh
                Show
                ann.loraine Ann Loraine added a comment - if the current working directory is not in your PATH, you need to specify the directory when you run the script, e.g., ./sbatch-doIt.sh
                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 -
                Assignee Ann Loraine [ aloraine ]
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                ann.loraine Ann Loraine added a comment -

                Before proceeding with deploying the data, need to check the multiqc reports.

                Show
                ann.loraine Ann Loraine added a comment - Before proceeding with deploying the data, need to check the multiqc reports.
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                Hide
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                Mdavis4290 Molly Davis added a comment -

                SRP268884 Scaled Coverage graphs have been updated and new multiqc report can be found in ticket:
                https://jira.bioviz.org/browse/IGBF-3228

                Show
                Mdavis4290 Molly Davis added a comment - SRP268884 Scaled Coverage graphs have been updated and new multiqc report can be found in ticket: https://jira.bioviz.org/browse/IGBF-3228
                ann.loraine Ann Loraine made changes -
                Sprint Spring 1 2023 Dec 26, Spring 2 2023 Jan 16 [ 161, 162 ] Spring 1 2023 Dec 26, Spring 2 2023 Jan 16, Spring 3 2023 Jan 30 [ 161, 162, 163 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Sprint Spring 1 2023 Dec 26, Spring 2 2023 Jan 16, Spring 3 2023 Feb 1 [ 161, 162, 163 ] Spring 1 2023 Dec 26, Spring 2 2023 Jan 16, Spring 3 2023 Feb 1, Spring 4 2023 Feb 21 [ 161, 162, 163, 164 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                Hide
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                ann.loraine Ann Loraine added a comment -

                Copied files to RENCI host. Moving to done.

                Show
                ann.loraine Ann Loraine added a comment - Copied files to RENCI host. Moving to done.
                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 ]

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: