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Vitis vinifera #607

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4 of 7 tasks
RaymondS1 opened this issue Jan 13, 2021 · 4 comments
Open
4 of 7 tasks

Vitis vinifera #607

RaymondS1 opened this issue Jan 13, 2021 · 4 comments

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@RaymondS1
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RaymondS1 commented Jan 13, 2021 •
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BioProject Checklist:

  • PRJNA524691
  • PRJNA513863
  • PRJNA488534
  • PRJNA309491

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.
@RaymondS1
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RaymondS1 commented Jan 14, 2021 •
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PRJNA524691
Location on the acf /lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/vitis_vinifera/PRJNA524691_ray
4 SRAs

  • fastq_dump
  • Run nextflow
    - All completed
  • calculate tpm
  • Load biosamples

@RaymondS1
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RaymondS1 commented Jan 14, 2021 •
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PRJNA513863
110 SRAs

  • fastq_dump
    - Not completed
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
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RaymondS1 commented Jan 14, 2021 •
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PRJNA488534
/lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/vitis_vinifera/PRJNA488534_ray
36 SRAs

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
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RaymondS1 commented Jan 14, 2021 •
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PRJNA309491
/lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/vitis_vinifera/PRJNA309491_ray
3 SRAs

  • fastq_dump
  • Run nextflow
    - All completed
  • calculate tpm
  • Load biosamples

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@RaymondS1