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  1. IGB
  2. IGBF-3376

Create scaled and junction files for 2021 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

          • Rename "sorted"
          • Make Scaled files
          • Make junction files

          Notes:
          SL5 junctions 2bit file: S_lycopersicum_Jun_2022.2bit
          SL4 junctions 2bit file: S_lycopersicum_Sep_2019.2bit

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              blocks

              Task - A task that needs to be done. IGBF-3377 Make 2021 Palanivelu to sample sheet

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

              Task - A task that needs to be done. IGBF-3375 Run Nextflow with 2021 Palanivelu Lab-generated samples

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

              Task - A task that needs to be done. IGBF-3389 Edit XML script to include SL4, SL5 tomato genomes

              • Major - Major loss of function.
              • Closed

                Activity

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                Mdavis4290 Molly Davis added a comment - - edited

                Launch Scaled Coverage graphs script: 

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

                Launch Junction files script: 

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

                SL5 Directory: /nobackup/tomato_genome/Ravi_tamaulipas_2021/Ravi_2021_SL5/results/star_salmon
                SL4 Directory: /nobackup/tomato_genome/Ravi_tamaulipas_2021/Ravi_2021_SL4/results/star_salmon

                Reviewer:

                • Check that files have reasonable sizes (no "zero" size files, for example)
                • Check that every "FJ.bed.gz" file has a corresponding "FJ.bed.gz.tbi" index file
                • Check that every bam file has a corresponding "FJ.bed.gz" file
                • If all files are normal please move ticket to done
                Show
                Mdavis4290 Molly Davis added a comment - - edited Launch Scaled Coverage graphs script : ./sbatch-doIt.sh .bam bamCoverage.sh >jobs.out 2>jobs.err Launch Junction files script : ./sbatch-doIt.sh .bam find_junctions.sh >jobs.out 2>jobs.err SL5 Directory : /nobackup/tomato_genome/Ravi_tamaulipas_2021/Ravi_2021_SL5/results/star_salmon SL4 Directory : /nobackup/tomato_genome/Ravi_tamaulipas_2021/Ravi_2021_SL4/results/star_salmon Reviewer : Check that files have reasonable sizes (no "zero" size files, for example) Check that every "FJ.bed.gz" file has a corresponding "FJ.bed.gz.tbi" index file Check that every bam file has a corresponding "FJ.bed.gz" file If all files are normal please move ticket to done
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                nfreese Nowlan Freese added a comment -

                Checked the SL5 and SL4 directory. Did not see any zero size files (bam/bed/bedgraph). Every bam file had a corresponding FJ.bed and scaled.bedgraph file as well as corresponding indices.

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - Checked the SL5 and SL4 directory. Did not see any zero size files (bam/bed/bedgraph). Every bam file had a corresponding FJ.bed and scaled.bedgraph file as well as corresponding indices. Closing ticket.

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    Mdavis4290 Molly Davis
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                    Dates

                    • Created:
                      Updated:
                      Resolved: