Populus trichocarpa - Expression Analyses

[MattHuff]

BioProject Checklist:

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• [x] PRJEB19784
• [x] PRJNA284202
• [x] PRJNA314500
• [x] PRJNA315705
• [x] PRJNA381918
• [x] PRJNA398322
• [x] PRJNA400507
• [x] PRJNA522886
• [x] PRJNA316974
• [x] PRJNA432076 - Note that only 9 of these samples are P. trichocarpa.
• [x] PRJNA304268
• [x] PRJNA300564
• [x] PRJNA237653 - One sample is not from P. trichocarpa.
• [x] PRJNA516861

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.

• [x] Use the python TPM script to normalize all counts files.
• [x] Load all biosamples onto the Hardwoods website.
• [x] Load the normalized counts files onto the Hardwoods website.

[RaymondS1]

PRJEB19784

• [x] prefetch (81 SRAa)
• [ ] convert to fastq
• [ ] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[patricksis]

PRJNA315705

• [x] prefetch (12 SRAa)
• [x] convert to fastq
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[patricksis]

PRJNA381918

• [x] prefetch (295 SRAa)
• [x] convert to fastq
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[patricksis]

PRJNA398322

• [x] prefetch (21 SRAa)
• [x] convert to fastq
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[CaseyRichards92]

PRJNA304268

• [x] convert to fastq
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[CaseyRichards92]

Analysis to use for p_trichocarpa biosamples https://hardwoodgenomics.org/Analysis/3958776

[RaymondS1]

PRJNA522886

• [x] prefetch (4 SRAs)
• [x] convert to fastq
• [ ] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[patricksis]

PRJNA316974

• [x] fastq_dump (12 SRAs)
• [x] convert to fastq
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[CaseyRichards92]

PRJNA516861

• [x] convert to fastq
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[patricksis]

PRJNA237653

• [x] fastq_dump (6 SRAs)
• [x] Run nextflow
• [x] calculate tpm
• [x] Load biosamples

[CaseyRichards92]

PRJNA300564

• [ ] fastq_dump
• [x] 1-100 SRA Casey
• [x] 101-200 SRA Casey
• [ ] 201-300 SRA
• [ ] 301-400 SRA
• [ ] 401-500 SRA
• [ ] 501-600 SRA
• [ ] 601-700 SRA
• [ ] 701-778 SRA
• [ ] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples
• [x] 1-100 Biosample Casey
• [x] 101-200 Biosample
• [x] 201-300 Biosample
• [x] 301-400 Biosample
• [x] 401-500 Biosample
• [x] 501-600 Biosample
• [x] 601-700 Biosample
• [x] 701-778 Biosample