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Malus Domestica #606

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5 of 8 tasks
RaymondS1 opened this issue Jan 6, 2021 · 5 comments
Open
5 of 8 tasks

Malus Domestica #606

RaymondS1 opened this issue Jan 6, 2021 · 5 comments

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@RaymondS1
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RaymondS1 commented Jan 6, 2021 •
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BioProject Checklist:

  • PRJNA493865
  • PRJNA374502
  • PRJNA339488
  • PRJNA306594
  • PRJDB6779

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 6, 2021 •
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PRJNA493865
Location on the acf /lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/malus_domestica/PRJNA493865_ray
6 SRAs

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

@RaymondS1
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RaymondS1 commented Jan 12, 2021 •
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PRJNA374502
/lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/malus_domestica/PRJNA374502_ray/analysis_SE
12 SRAs

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

@RaymondS1
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RaymondS1 commented Jan 12, 2021 •
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PRJNA339488
/lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/malus_domestica/PRJNA339488_ray
2 SRAs

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
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RaymondS1 commented Jan 12, 2021 •
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PRJNA306594
/lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/malus_domestica/PRJNA306594_ray
8 SRAs

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
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RaymondS1 commented Jan 12, 2021 •
edited
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PRJDB6779
/lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/malus_domestica/PRJDB6779/analysis
28 SRAs

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

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@RaymondS1