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  1. IGB
  2. IGBF-3162

Generate scaled coverage graphs for RNA-Seq alignments

        Details

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

          Description

          Make scaled coverages graphs for the alternative splicing project BAM files.

            Attachments

              Issue Links

              blocks

              Task - A task that needs to be done. IGBF-3144 Make annots.xml for RNA-Seq junction, alignment, and coverage graphs

              • Major - Major loss of function.
              • Closed
              is blocked by

              Task - A task that needs to be done. IGBF-3163 Rename or create symbolic links to BAM alignments files to remove "sorted" in the file names

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

              Task - A task that needs to be done. IGBF-3143 Run RNA-Seq data processing pipeline on positive splicing control and experimental samples

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3239 Create scaled coverage graphs for SRP100604 and SRP268884

              • 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-3143 [ IGBF-3143 ]
                ann.loraine Ann Loraine made changes -
                Link This issue blocks IGBF-3144 [ IGBF-3144 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Link This issue is blocked by IGBF-3163 [ IGBF-3163 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 1 2022 Aug 15 [ 153 ] Fall 1 2022 Aug 15, Fall 2 2022 Sep 5 [ 153, 154 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
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                ann.loraine Ann Loraine added a comment - - edited

                Added scripts to new repository hotpollen/splicing-analysis.
                Created new directory:

                /nobackup/tomato_genome/alt_splicing/coverage_graph_bams

                in UNCC cluster with symbolic links to bam files made in IGBF-3143 and IGBF-3163.

                Made symbolic links to code in my home directory for generating coverage graphs. Launched jobs with:

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

                Seems to be running OK.

                Scripts used:

                • src/sbatch-doIt.sh
                • src/bamCoverage.sh

                in repository https://bitbucket.org/hotpollen/splicing-analysis

                Show
                ann.loraine Ann Loraine added a comment - - edited Added scripts to new repository hotpollen/splicing-analysis. Created new directory: /nobackup/tomato_genome/alt_splicing/coverage_graph_bams in UNCC cluster with symbolic links to bam files made in IGBF-3143 and IGBF-3163 . Made symbolic links to code in my home directory for generating coverage graphs. Launched jobs with: sbatch-doIt.sh .bam bamCoverage.sh >jobs.out 2>jobs.err Seems to be running OK. Scripts used: src/sbatch-doIt.sh src/bamCoverage.sh in repository https://bitbucket.org/hotpollen/splicing-analysis
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
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                ann.loraine Ann Loraine added a comment - - edited

                Files are done.

                I moved them to /nobackup/tomato_genome/alt_splicing/for_igbquickload/coverage_graphs.

                To review:

                • check that files have reasonable sizes (nothing non-zero)
                • check that every ".scaled.bedgraph.gz" file has a corresponding ".scaled.bedgraph.gz.tbi" index file
                • check that every "SRR" bam file in our control and experimental sample directories has a corresponding "scaled.bedgraph.gz" file
                Show
                ann.loraine Ann Loraine added a comment - - edited Files are done. I moved them to /nobackup/tomato_genome/alt_splicing/for_igbquickload/coverage_graphs. To review: check that files have reasonable sizes (nothing non-zero) check that every ".scaled.bedgraph.gz" file has a corresponding ".scaled.bedgraph.gz.tbi" index file check that every "SRR" bam file in our control and experimental sample directories has a corresponding "scaled.bedgraph.gz" file
                Hide
                Permalink
                Mdavis4290 Molly Davis added a comment - - edited

                Review:

                Directory- /nobackup/tomato_genome/alt_splicing/for_igbquickload/coverage_graphs

                • No files seemed to have zero file size. Used command LL/ll.
                • Every ".scaled.bedgraph.gz" file has a ".scaled.bedgraph.gz.tbi" file.
                • Every "SRR" bam file in our control and experimental sample directories has a corresponding "scaled.bedgraph.gz" file. SRP328042-molly SRR files are in-between SRP252265 files in the directory might be hard to differentiate which is control and which is experimental.

                [~aloraine]

                Show
                Mdavis4290 Molly Davis added a comment - - edited Review: Directory- /nobackup/tomato_genome/alt_splicing/for_igbquickload/coverage_graphs No files seemed to have zero file size. Used command LL/ll. Every ".scaled.bedgraph.gz" file has a ".scaled.bedgraph.gz.tbi" file. Every "SRR" bam file in our control and experimental sample directories has a corresponding "scaled.bedgraph.gz" file. SRP328042-molly SRR files are in-between SRP252265 files in the directory might be hard to differentiate which is control and which is experimental. [~aloraine]
                Hide
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                ann.loraine Ann Loraine added a comment -

                Thanks [~molly]. I decided to store all the files in the same folder and will use an index / table of contents type strategy to distinguish them. Moving to Done.

                Show
                ann.loraine Ann Loraine added a comment - Thanks [~molly] . I decided to store all the files in the same folder and will use an index / table of contents type strategy to distinguish them. 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 Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3239 [ IGBF-3239 ]
                ann.loraine Ann Loraine made changes -
                Description Run bamCoverage script to generate scaled coverages graphs for the alternative splicing project BAM files.

                For an example of how to do this, please see:

                * bamCoverage.sh
                * sbatch-doIt.sh

                in:

                https://bitbucket.org/hotpollen/flavonoid-rnaseq/src
                		Run bamCoverage script to generate scaled coverages graphs for the alternative splicing project BAM files.

                ann.loraine Ann Loraine made changes -
                Description Run bamCoverage script to generate scaled coverages graphs for the alternative splicing project BAM files.

                		Make scaled coverages graphs for the alternative splicing project BAM files.

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: