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  1. IGB
  2. IGBF-3390

Run Nextflow with 2022 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

          Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq

          • Run nextflow for SL4 &SL5
          • create sample CSV
          • Check Mulitqc report for strandedness
          • Commit multiqc reports and sample.csv (Ravi_sample_2022.csv)

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              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3391 Create scaled and junction files for 2022 Palanivelu Lab-generated samples

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3392 Make sample sheet for 2022 Palanivelu

              • 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 -
                Link This issue relates to IGBF-3367 [ IGBF-3367 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3391 [ IGBF-3391 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3392 [ IGBF-3392 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Summary Run Nextflow with 2022 Palanavelu Lab-generated samples Run Nextflow with 2022 Palanivelu Lab-generated samples
                Mdavis4290 Molly Davis made changes -
                Description Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq
                Nf-core run: /nobackup/tomato_genome/ravi-55/sl5-nfcore/results # but there are no scaled or junction files.

                * Nextflow SL4 & SL5 have already been created with nf-core
                * Should I rerun?
                * Need to commit multiqc reports?                 		Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq

                * Run nextflow for SL4 &SL5
                * create sample CSV
                * Check Mulitqc report for strandedness
                * Commit multiqc reports
                Hide
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                Mdavis4290 Molly Davis added a comment - - edited

                Directory: /nobackup/tomato_genome/Ravi_2022

                Notes: Had to rerun because strandedness was reverse not unstranded after reviewing the multiqc report.

                SL4 command & 2019 data: 

                ./doIt.sh Ravi_samples_2022.csv /nobackup/tomato_genome/nfcore_rnaseq/S_lycopersicum_Sep_2019.fa /nobackup/tomato_genome/nfcore_rnaseq/S_lycopersicum_Sep_2019.gtf /nobackup/tomato_genome/nfcore_rnaseq/S_lycopersicum_Sep_2019.bed tomato.config 1> out.0.txt 2> err.0.txt
                Show
                Mdavis4290 Molly Davis added a comment - - edited Directory : /nobackup/tomato_genome/Ravi_2022 Notes: Had to rerun because strandedness was reverse not unstranded after reviewing the multiqc report. SL4 command & 2019 data: ./doIt.sh Ravi_samples_2022.csv /nobackup/tomato_genome/nfcore_rnaseq/S_lycopersicum_Sep_2019.fa /nobackup/tomato_genome/nfcore_rnaseq/S_lycopersicum_Sep_2019.gtf /nobackup/tomato_genome/nfcore_rnaseq/S_lycopersicum_Sep_2019.bed tomato.config 1> out.0.txt 2> err.0.txt
                Mdavis4290 Molly Davis made changes -
                Description Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq

                * Run nextflow for SL4 &SL5
                * create sample CSV
                * Check Mulitqc report for strandedness
                * Commit multiqc reports                 		Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq

                * Run nextflow for SL4 &SL5
                * create sample CSV
                * Check Mulitqc report for strandedness
                * Commit multiqc reports and sample.csv (Ravi_sample_2022.csv)
                ann.loraine Ann Loraine made changes -
                Sprint Summer 5 2023 July 10 [ 174 ] Summer 5 2023 July 10, Summer 6 2023 July 24 [ 174, 175 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
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                Mdavis4290 Molly Davis added a comment - - edited

                MultiQC Report Notes:

                SL5 seemed to have no issues with strandedness after changing it to 'reverse'. I used the same sample.CSV file for the SL4 genome and ran nextflow and there seemed to be a strandedness warning on the mulitqc report. This happened for the 2021 data as well and I am unsure why these strandedness warning keep occurring. There are no issues with strandedness for the SL5 genome.

                Next step: I will keep the multiqc report how it is and commit the files so they can be reviewed.

                Show
                Mdavis4290 Molly Davis added a comment - - edited MultiQC Report Notes : SL5 seemed to have no issues with strandedness after changing it to 'reverse'. I used the same sample.CSV file for the SL4 genome and ran nextflow and there seemed to be a strandedness warning on the mulitqc report. This happened for the 2021 data as well and I am unsure why these strandedness warning keep occurring. There are no issues with strandedness for the SL5 genome. Next step: I will keep the multiqc report how it is and commit the files so they can be reviewed.
                Hide
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                ann.loraine Ann Loraine added a comment -

                Double-check that the gene model annotations are correct. These are the gtf, bed, gff etc files used.

                Show
                ann.loraine Ann Loraine added a comment - Double-check that the gene model annotations are correct. These are the gtf, bed, gff etc files used.
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
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                Mdavis4290 Molly Davis added a comment - - edited

                Checking SL4 annotation files:
                Directory- /nobackup/tomato_genome/nfcore_rnaseq

                I see no issues with the files themselves. Each contains annotations for the SL4 genome.

                Next step: commit multiqc reports and sample.csv file.

                Show
                Mdavis4290 Molly Davis added a comment - - edited Checking SL4 annotation files : Directory- /nobackup/tomato_genome/nfcore_rnaseq I see no issues with the files themselves. Each contains annotations for the SL4 genome. Next step: commit multiqc reports and sample.csv file.
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 5 2023 July 10, Summer 6 2023 July 24 [ 174, 175 ] Summer 5 2023 July 10, Summer 6 2023 July 24, Summer 7 2023 Aug 7 [ 174, 175, 176 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                Hide
                Permalink
                Mdavis4290 Molly Davis added a comment -

                Branch: https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3390

                Note: Moved 2021 sample sheet to ExternalData folder as well as add the reports and csv file.

                Show
                Mdavis4290 Molly Davis added a comment - Branch : https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3390 Note: Moved 2021 sample sheet to ExternalData folder as well as add the reports and csv file.
                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 -

                Ready for pull request. Please submit PR when ready.

                Show
                ann.loraine Ann Loraine added a comment - Ready for pull request. Please submit PR when ready.
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                Hide
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                Mdavis4290 Molly Davis added a comment -

                Pull request: https://bitbucket.org/hotpollen/pistil-rna-seq/pull-requests/7

                Show
                Mdavis4290 Molly Davis added a comment - Pull request : https://bitbucket.org/hotpollen/pistil-rna-seq/pull-requests/7
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                Mdavis4290 Molly Davis 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 -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                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 ]

                  People

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

                    • Created:
                      Updated:
                      Resolved: