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  1. IGB
  2. IGBF-3250

Process muday-144 RNA-Seq data

        Details

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

          Description

          Rob has run nf-core rnaseq pipeline using SL4 and SL5 genome assemblies. Results are in: /nobackup/tomato_genome/muday-144/.

          For this task, complete RNA-Seq data processing:

          • Review QC file
          • Collect BAM files (removing "sorted" from the names)
          • Make scaled coverage graphs
          • Make junction files
          • Enter key data files into flavonoid-rnaseq repository - QC report, samples.csv used to run the pipeline, gene counts file, etc
          • Create sample description file for statistical analysis and Quickload metadata file generation
          • Deploy data files to Quickload for hosting

          Flavonoid RNA-Seq git repository: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/ (currently private)

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              relates to

              Task - A task that needs to be done. IGBF-3262 Make Markdown showing DESeq analysis of Muday time course SL5 data

              • Major - Major loss of function.
              • Closed

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                4 older comments
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                ann.loraine Ann Loraine added a comment - - edited

                When making coverage graphs, one of the jobs failed. Here is the error file:

                [aloraine@str-i1 coverage_graphs2]$ cat 8-are-75-min-28C.err
                /var/spool/slurm/slurmd/job386205/slurm_script: line 9: module: command not found
                /var/spool/slurm/slurmd/job386205/slurm_script: line 10: module: command not found
                /var/spool/slurm/slurmd/job386205/slurm_script: line 21: bamCoverage: command not found
                /var/spool/slurm/slurmd/job386205/slurm_script: line 22: bgzip: command not found
                /var/spool/slurm/slurmd/job386205/slurm_script: line 25: tabix: command not found
                [aloraine@str-i1 coverage_graphs2]$

                Re-running the batch job submission after removing links to bam files already processed.

                Show
                ann.loraine Ann Loraine added a comment - - edited When making coverage graphs, one of the jobs failed. Here is the error file: [aloraine@str-i1 coverage_graphs2] $ cat 8-are-75-min-28C.err /var/spool/slurm/slurmd/job386205/slurm_script: line 9: module: command not found /var/spool/slurm/slurmd/job386205/slurm_script: line 10: module: command not found /var/spool/slurm/slurmd/job386205/slurm_script: line 21: bamCoverage: command not found /var/spool/slurm/slurmd/job386205/slurm_script: line 22: bgzip: command not found /var/spool/slurm/slurmd/job386205/slurm_script: line 25: tabix: command not found [aloraine@str-i1 coverage_graphs2] $ Re-running the batch job submission after removing links to bam files already processed.
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                ann.loraine Ann Loraine added a comment - - edited

                For some reason, multiqc report did not get made for the SL5 genome assembly (2022). MD looking into it. Also, a problem with SL4 (2019) run.for the moment.

                Follow-up: We decided to not align against SL4 genome assembly Tabling that task.

                Show
                ann.loraine Ann Loraine added a comment - - edited For some reason, multiqc report did not get made for the SL5 genome assembly (2022). MD looking into it. Also, a problem with SL4 (2019) run.for the moment. Follow-up: We decided to not align against SL4 genome assembly Tabling that task.
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                ann.loraine Ann Loraine added a comment - - edited

                Deployed alignment files, coverage graphs, and junction files to igb quickload location: /projects/igbquickload/lorainelab/www/main/htdocs/hotpollen/S_lycopersicum_Jun_2022/muday-2022-timeseries

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                ann.loraine Ann Loraine added a comment - - edited Deployed alignment files, coverage graphs, and junction files to igb quickload location: /projects/igbquickload/lorainelab/www/main/htdocs/hotpollen/S_lycopersicum_Jun_2022/muday-2022-timeseries
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                Mdavis4290 Molly Davis added a comment - - edited

                Update:
                Nextflow successfully ran for muday-2022:

                Directory: /nobackup/tomato_genome/muday-144/nfcore-2022

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                Mdavis4290 Molly Davis added a comment - - edited Update: Nextflow successfully ran for muday-2022: Directory: /nobackup/tomato_genome/muday-144/nfcore-2022 Check new multiqc report: muday22_multiqc_report.html Comment: No more issues with strandedness and everything else looks fine!
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                ann.loraine Ann Loraine added a comment -

                All tasks are complete, including deployment of alignment files (bam), scaled coverage graphs (bedgraph), and junction files (bed12) to Web hosting.
                Moving to Done.

                Show
                ann.loraine Ann Loraine added a comment - All tasks are complete, including deployment of alignment files (bam), scaled coverage graphs (bedgraph), and junction files (bed12) to Web hosting. Moving to Done.

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    ann.loraine Ann Loraine
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                    • Created:
                      Updated:
                      Resolved: