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Vitis vinifera - expression analysis #595

Open
24 of 27 tasks
MattHuff opened this issue Jul 6, 2020 · 25 comments
Open
24 of 27 tasks

Vitis vinifera - expression analysis #595

MattHuff opened this issue Jul 6, 2020 · 25 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:

  • PRJNA550508
  • PRJNA529179
  • PRJNA528770
  • PRJNA524691
  • PRJNA521303
  • PRJNA516950
  • PRJNA508364
  • PRJNA488534
  • PRJNA476839
  • PRJNA472397
  • PRJNA433817
  • PRJNA418785
  • PRJNA402079
  • PRJNA395634
  • PRJNA390670
  • PRJNA163649
  • PRJNA350310
  • PRJNA348618
  • PRJNA336064
  • PRJNA320028
  • PRJNA312428
  • PRJNA313234
  • PRJNA309491
  • PRJEB30338

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 Jul 13, 2020 •
edited
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PRJNA550508

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
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RaymondS1 commented Jul 13, 2020 •
edited
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PRJNA529179

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
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RaymondS1 commented Jul 13, 2020 •
edited
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PRJNA528770

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
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RaymondS1 commented Jul 19, 2020 •
edited
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PRJNA524691

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
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RaymondS1 commented Jul 19, 2020 •
edited
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PRJNA521303

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
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RaymondS1 commented Jul 20, 2020 •
edited
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PRJNA516950

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
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RaymondS1 commented Jul 26, 2020 •
edited
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PRJNA508364

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
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RaymondS1 commented Jul 27, 2020 •
edited
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PRJNA488534

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
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RaymondS1 commented Jul 27, 2020 •
edited
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PRJNA476839 (both single and paired)

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

@RaymondS1
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RaymondS1 commented Jul 28, 2020 •
edited
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PRJNA472397 (not outputing)

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

@RaymondS1
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RaymondS1 commented Jul 28, 2020 •
edited
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PRJNA433817

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

@RaymondS1
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RaymondS1 commented Aug 3, 2020 •
edited
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PRJNA418785

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

@RaymondS1
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RaymondS1 commented Aug 5, 2020 •
edited
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PRJNA402079

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

@RaymondS1
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RaymondS1 commented Aug 5, 2020 •
edited
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PRJNA395634

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

@RaymondS1
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RaymondS1 commented Aug 5, 2020 •
edited
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PRJNA390670

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

@RaymondS1
Copy link

RaymondS1 commented Aug 5, 2020 •
edited
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PRJNA163649

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

@RaymondS1
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RaymondS1 commented Aug 5, 2020 •
edited
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PRJNA350310

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

@CaseyRichards92
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CaseyRichards92 commented Aug 5, 2020 •
edited
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PRJEB30338

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

@RaymondS1
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RaymondS1 commented Aug 5, 2020 •
edited
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PRJNA348618

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

@CaseyRichards92
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CaseyRichards92 commented Aug 6, 2020 •
edited
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PRJNA309491

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

@CaseyRichards92
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Gene Atlas https://hardwoodgenomics.org/Gene-expression-profiling/4244032

@CaseyRichards92
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CaseyRichards92 commented Aug 19, 2020 •
edited
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PRJNA313234

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

@RaymondS1
Copy link

RaymondS1 commented Aug 19, 2020 •
edited
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PRJNA320028

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

@RaymondS1
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RaymondS1 commented Aug 19, 2020 •
edited
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PRJNA312428

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

@CaseyRichards92
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CaseyRichards92 commented Aug 20, 2020 •
edited
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PRJNA336064

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosample

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@patricksis patricksis

@CaseyRichards92 CaseyRichards92

@RaymondS1 RaymondS1

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data upload Load into Chado Undergraduate Task
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@MattHuff @patricksis @CaseyRichards92 @RaymondS1