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  1. IGB
  2. IGBF-3242

Run nextflow for seedlingPollen dataset

        Details

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

          Description

          Re-run nextflow rnaseq pipeline in:

          /nobackup/tomato_genome/seedlingPollen/nfcore

          Using new samples.csv file with "reverse" in the strandedness field.

          Please just edit "samples.csv" in /nobackup/tomato_genome/seedlingPollen/nfcore.

          Note about sample names:

          MP - mature pollen
          Se - seedling
          N - nagcarlang
          H - heinz
          T - tamaulipas
          M - malintka
          S - stress
          C - control

          See folder in the google drive with info about the experiment:

          • Experiments > Pollen Grain and Seedling RNA-seq

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              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3246 Generate list of EBSeq-HMM clusters for varieties and conditions

              • 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 -
                Description * Get data from google drive onto the cluster
                * Migrate data from cluster to an igbquickload host
                		* Get data from google drive onto the cluster
                * Migrate data from cluster to an igbquickload host

                See: https://drive.google.com/drive/folders/1eHn-uK6N5PEr3fr8kfWHrySrarx5XOYU?usp=share_link
                ann.loraine Ann Loraine made changes -
                Description * Get data from google drive onto the cluster
                * Migrate data from cluster to an igbquickload host

                See: https://drive.google.com/drive/folders/1eHn-uK6N5PEr3fr8kfWHrySrarx5XOYU?usp=share_link                 		* Get data from google drive onto the cluster
                * Migrate data from cluster to an igbquickload host

                See: https://drive.google.com/drive/folders/1GJnZefP-7TE-ch-c0lblGZMOqpwSgZRK?usp=share_link
                ann.loraine Ann Loraine made changes -
                Summary Deploy new Dec 2022 data onto an igbquickload site Run nextflow for mark-2022-timeseries
                ann.loraine Ann Loraine made changes -
                Description * Get data from google drive onto the cluster
                * Migrate data from cluster to an igbquickload host

                See: https://drive.google.com/drive/folders/1GJnZefP-7TE-ch-c0lblGZMOqpwSgZRK?usp=share_link                 		Run nextflow nfcore rnaseq pipeline on fastq files in:

                /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

                ann.loraine Ann Loraine made changes -
                Description Run nextflow nfcore rnaseq pipeline on fastq files in:

                /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

                		Re-run nextflow rnaseq pipeline in:

                /nobackup/tomato_genome/seedlingPollen/nfcore

                Using new samples.csv file with "reverse" in the strandedness

                ann.loraine Ann Loraine made changes -
                Summary Run nextflow for mark-2022-timeseries Run nextflow for seedlingPollen dataset
                ann.loraine Ann Loraine made changes -
                Description Re-run nextflow rnaseq pipeline in:

                /nobackup/tomato_genome/seedlingPollen/nfcore

                Using new samples.csv file with "reverse" in the strandedness

                		Re-run nextflow rnaseq pipeline in:

                /nobackup/tomato_genome/seedlingPollen/nfcore

                Using new samples.csv file with "reverse" in the strandedness field.

                Please just edit "samples.csv" in /nobackup/tomato_genome/seedlingPollen/nfcore.

                Note about sample names:

                MP - mature pollen
                Se - seedling
                N - nagcarlang
                H - heinz
                T - tamalipas

                S - heat-treated, 34 degrees
                C - non-heated treated, raised at 28 degrees

                ann.loraine Ann Loraine made changes -
                Description Re-run nextflow rnaseq pipeline in:

                /nobackup/tomato_genome/seedlingPollen/nfcore

                Using new samples.csv file with "reverse" in the strandedness field.

                Please just edit "samples.csv" in /nobackup/tomato_genome/seedlingPollen/nfcore.

                Note about sample names:

                MP - mature pollen
                Se - seedling
                N - nagcarlang
                H - heinz
                T - tamalipas

                S - heat-treated, 34 degrees
                C - non-heated treated, raised at 28 degrees

                		Re-run nextflow rnaseq pipeline in:

                /nobackup/tomato_genome/seedlingPollen/nfcore

                Using new samples.csv file with "reverse" in the strandedness field.

                Please just edit "samples.csv" in /nobackup/tomato_genome/seedlingPollen/nfcore.

                Note about sample names:

                MP - mature pollen
                Se - seedling
                N - nagcarlang
                H - heinz
                T - tamalipas
                M - malintka
                S - heat-treated, 37 degrees
                C - non-heated treated, raised at 28 degrees

                See "experiment" folder in the google drive

                ann.loraine Ann Loraine made changes -
                Description Re-run nextflow rnaseq pipeline in:

                /nobackup/tomato_genome/seedlingPollen/nfcore

                Using new samples.csv file with "reverse" in the strandedness field.

                Please just edit "samples.csv" in /nobackup/tomato_genome/seedlingPollen/nfcore.

                Note about sample names:

                MP - mature pollen
                Se - seedling
                N - nagcarlang
                H - heinz
                T - tamalipas
                M - malintka
                S - heat-treated, 37 degrees
                C - non-heated treated, raised at 28 degrees

                See "experiment" folder in the google drive

                		Re-run nextflow rnaseq pipeline in:

                /nobackup/tomato_genome/seedlingPollen/nfcore

                Using new samples.csv file with "reverse" in the strandedness field.

                Please just edit "samples.csv" in /nobackup/tomato_genome/seedlingPollen/nfcore.

                Note about sample names:

                MP - mature pollen
                Se - seedling
                N - nagcarlang
                H - heinz
                T - tamalipas
                M - malintka
                S - heat-treated, 37 degrees
                C - non-heated treated, raised at 28 degrees

                See "experiment" folder in the google drive with info about the experiment:

                Experiments > Pollen Grain and Seedling RNA-seq > SRA Description - pollen grain and seedling experiments


                ann.loraine Ann Loraine made changes -
                Description Re-run nextflow rnaseq pipeline in:

                /nobackup/tomato_genome/seedlingPollen/nfcore

                Using new samples.csv file with "reverse" in the strandedness field.

                Please just edit "samples.csv" in /nobackup/tomato_genome/seedlingPollen/nfcore.

                Note about sample names:

                MP - mature pollen
                Se - seedling
                N - nagcarlang
                H - heinz
                T - tamalipas
                M - malintka
                S - heat-treated, 37 degrees
                C - non-heated treated, raised at 28 degrees

                See "experiment" folder in the google drive with info about the experiment:

                Experiments > Pollen Grain and Seedling RNA-seq > SRA Description - pollen grain and seedling experiments


                		Re-run nextflow rnaseq pipeline in:

                /nobackup/tomato_genome/seedlingPollen/nfcore

                Using new samples.csv file with "reverse" in the strandedness field.

                Please just edit "samples.csv" in /nobackup/tomato_genome/seedlingPollen/nfcore.

                Note about sample names:

                MP - mature pollen
                Se - seedling
                N - nagcarlang
                H - heinz
                T - tamaulipas
                M - malintka
                S - heat-treated, 37 degrees
                C - non-heated treated, raised at 28 degrees

                See "experiment" folder in the google drive with info about the experiment:

                Experiments > Pollen Grain and Seedling RNA-seq > SRA Description - pollen grain and seedling experiments


                ann.loraine Ann Loraine made changes -
                Story Points 1 0.5
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                ann.loraine Ann Loraine made changes -
                Description Re-run nextflow rnaseq pipeline in:

                /nobackup/tomato_genome/seedlingPollen/nfcore

                Using new samples.csv file with "reverse" in the strandedness field.

                Please just edit "samples.csv" in /nobackup/tomato_genome/seedlingPollen/nfcore.

                Note about sample names:

                MP - mature pollen
                Se - seedling
                N - nagcarlang
                H - heinz
                T - tamaulipas
                M - malintka
                S - heat-treated, 37 degrees
                C - non-heated treated, raised at 28 degrees

                See "experiment" folder in the google drive with info about the experiment:

                Experiments > Pollen Grain and Seedling RNA-seq > SRA Description - pollen grain and seedling experiments


                		Re-run nextflow rnaseq pipeline in:

                /nobackup/tomato_genome/seedlingPollen/nfcore

                Using new samples.csv file with "reverse" in the strandedness field.

                Please just edit "samples.csv" in /nobackup/tomato_genome/seedlingPollen/nfcore.

                Note about sample names:

                MP - mature pollen
                Se - seedling
                N - nagcarlang
                H - heinz
                T - tamaulipas
                M - malintka
                S - stress
                C - control

                See folder in the google drive with info about the experiment:

                * Experiments > Pollen Grain and Seedling RNA-seq


                Mdavis4290 Molly Davis made changes -
                Attachment Screen Shot 2023-01-18 at 3.35.37 PM.png [ 17653 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis made changes -
                Attachment nfcore_multiqc_report.html [ 17657 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Attachment MichelleMedina-RNA-seq-Sample-Collection-pollen_grain-seedling.pdf [ 17668 ]
                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 ] Molly Davis [ molly ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3246 [ IGBF-3246 ]

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: