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  1. IGB
  2. IGBF-3086

Describe next steps for rice results

    Details

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

      Task: Determine and describe the next steps for the rice splicing and methylation data and paper.

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          nfreese Nowlan Freese created issue -
          nfreese Nowlan Freese made changes -
          Field Original Value New Value
          Epic Link IGBF-3039 [ 21553 ]
          nfreese Nowlan Freese made changes -
          Status To-Do [ 10305 ] In Progress [ 3 ]
          nfreese Nowlan Freese made changes -
          Status In Progress [ 3 ] To-Do [ 10305 ]
          nfreese Nowlan Freese made changes -
          Status To-Do [ 10305 ] In Progress [ 3 ]
          Hide
          nfreese Nowlan Freese added a comment - - edited

          Write paper:
          Abstract
          Introduction
          Materials and Methods
          Results
          Discussion
          Data availability, author contributions, funding, conflict of interest, acknowledgements
          References
          Assemble figures and legends

          Additional information:

          Show
          nfreese Nowlan Freese added a comment - - edited Write paper: Abstract Introduction Materials and Methods Results Discussion Data availability, author contributions, funding, conflict of interest, acknowledgements References Assemble figures and legends Additional information: Google Drive folder for initial paper (once we are closer to submission we will move it to Dropbox): https://drive.google.com/drive/folders/1reCWmYj7jnIYPjy9PHT1KtURPrCSUnyG?usp=sharing Special issue submission site for Frontiers: https://www.frontiersin.org/research-topics/24549/regulation-of-alternative-splicing-in-plant-stress-responses Example paper from Frontiers (where we may submit): https://www.frontiersin.org/articles/10.3389/fpls.2021.765003/full Author guidelines for Frontiers: https://www.frontiersin.org/about/author-guidelines
          Hide
          nfreese Nowlan Freese added a comment - - edited

          Generate files:
          RNA-Seq: bam/bai, bedgraph scaled, junctions

          • The NF-core pipeline most likely did not output bedgraph or junctions files (double-check on the cluster), so we will need to determine the best way to produce those files.
          • There should be a read counts file in the salmon folder on the cluster. Need to pull it down so we can use it to rerun the differential expression analysis.

          Many of the BS-Seq files are already in the quickload, but need to catalog those in the quickload and bitbucket:
          BS-Seq: bam/bai, bed (DMR regions), bedgraph (methyldackel)

          Show
          nfreese Nowlan Freese added a comment - - edited Generate files: RNA-Seq: bam/bai, bedgraph scaled, junctions The NF-core pipeline most likely did not output bedgraph or junctions files (double-check on the cluster), so we will need to determine the best way to produce those files. There should be a read counts file in the salmon folder on the cluster. Need to pull it down so we can use it to rerun the differential expression analysis. Many of the BS-Seq files are already in the quickload, but need to catalog those in the quickload and bitbucket: BS-Seq: bam/bai, bed (DMR regions), bedgraph (methyldackel)
          Hide
          nfreese Nowlan Freese added a comment -

          Upload new RNA-Seq files to quickload: http://lorainelab-quickload.scidas.org/saltyrice/
          Confirm that all files are viewable in the rice O_sativa_japonica_Oct_2011 genome

          Show
          nfreese Nowlan Freese added a comment - Upload new RNA-Seq files to quickload: http://lorainelab-quickload.scidas.org/saltyrice/ Confirm that all files are viewable in the rice O_sativa_japonica_Oct_2011 genome
          nfreese Nowlan Freese made changes -
          Status In Progress [ 3 ] To-Do [ 10305 ]
          nfreese Nowlan Freese made changes -
          Status To-Do [ 10305 ] In Progress [ 3 ]
          Hide
          nfreese Nowlan Freese added a comment - - edited

          The following tickets have been created:

          IGBF-3091 Write Introduction
          IGBF-3092 Write Materials and Methods
          IGBF-3093 Write Discussion
          IGBF-3094 Write Abstract
          IGBF-3095 Assemble figures and legends
          IGBF-3096 Assemble endnote library
          IGBF-3097 Generate RNA-Seq bedgraph scaled files
          IGBF-3098 Generate RNA-Seq junctions files
          IGBF-3099 Analyze differential expression using RNA-Seq
          IGBF-3100 Upload RNA-Seq files to Quickload
          IGBF-3101 Catalog current results for BS-Seq data
          IGBF-3102 Analyze differential splicing using RNA-Seq

          Show
          nfreese Nowlan Freese added a comment - - edited The following tickets have been created: IGBF-3091 Write Introduction IGBF-3092 Write Materials and Methods IGBF-3093 Write Discussion IGBF-3094 Write Abstract IGBF-3095 Assemble figures and legends IGBF-3096 Assemble endnote library IGBF-3097 Generate RNA-Seq bedgraph scaled files IGBF-3098 Generate RNA-Seq junctions files IGBF-3099 Analyze differential expression using RNA-Seq IGBF-3100 Upload RNA-Seq files to Quickload IGBF-3101 Catalog current results for BS-Seq data IGBF-3102 Analyze differential splicing using RNA-Seq
          nfreese Nowlan Freese made changes -
          Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
          nfreese Nowlan Freese made changes -
          Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
          nfreese Nowlan Freese made changes -
          Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
          nfreese Nowlan Freese made changes -
          Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
          nfreese Nowlan Freese made changes -
          Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
          nfreese Nowlan Freese made changes -
          Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
          nfreese Nowlan Freese made changes -
          Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
          nfreese Nowlan Freese made changes -
          Resolution Done [ 10000 ]
          Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
          Hide
          nfreese Nowlan Freese added a comment - - edited

          Additional tasks will be necessary to better define the specific results required for the paper. IGBF-3045 has potential ideas for results.

          Closing ticket.

          Show
          nfreese Nowlan Freese added a comment - - edited Additional tasks will be necessary to better define the specific results required for the paper. IGBF-3045 has potential ideas for results. Closing ticket.

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            • Assignee:
              nfreese Nowlan Freese
              Reporter:
              nfreese Nowlan Freese
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                Updated:
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