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Juglans nigra - expression analyses #593

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MattHuff opened this issue Jul 6, 2020 · 5 comments
Open
2 of 5 tasks

Juglans nigra - expression analyses #593

MattHuff opened this issue Jul 6, 2020 · 5 comments
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@patricksis @CaseyRichards92 @RaymondS1
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data upload Load into Chado Undergraduate Task

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@MattHuff
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MattHuff commented Jul 6, 2020 •
edited by CaseyRichards92
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BioProject Checklist:

  • PRJNA273267
  • PRJNA436029

Follow the Gene Expression Protocols on each of the SRAs in each Bioproject, but do not run TPM normalization on them until the pipeline has been run on all BioProjects.

  • Use the python TPM script to normalize all counts files.
  • Load all biosamples onto the Hardwoods website.
  • Load the normalized counts files onto the Hardwoods website.
@CaseyRichards92
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CaseyRichards92 commented Jul 6, 2020 •
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PRJNA273267

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
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CaseyRichards92 commented Jul 8, 2020 •
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PRJNA436029

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
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Biosample loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/896811
Published Biosamples https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/896812

@CaseyRichards92
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Expression loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/896816

@CaseyRichards92
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@almasaeed2010 @noahcaldwell7 Expression looks like it loaded correctly https://hardwoodgenomics.org/feature/Juglansnigra120313comp30759c0seq1?tripal_pane=group_expression

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@patricksis patricksis

@CaseyRichards92 CaseyRichards92

@RaymondS1 RaymondS1

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@MattHuff @patricksis @CaseyRichards92 @RaymondS1