Juglans nigra - expression analyses

[MattHuff]

BioProject Checklist:

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• [x] PRJNA273267
• [x] 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]

PRJNA273267

• [x] fastq_dump
• [x] Run nextflow
• [x] calculate tpm
• [ ] Load biosamples

[CaseyRichards92]

PRJNA436029

• [x] fastq_dump
• [x] Run nextflow
• [x] calculate tpm
• [ ] Load biosamples

[CaseyRichards92]

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

[CaseyRichards92]

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

[CaseyRichards92]

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