Prunus persica - expression analysis

[RaymondS1]

BioProject Checklist:

---

• PRJNA526626
• PRJNA567655

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]

PRJNA526626
(16 files)

• fastq_dump
  - failed to download SRR8713333 SRR8713341 SRR8713342 SRR8713343
  - All downloaded
• Run nextflow
  - 7 of 16 completed (currently rerunning)
  /lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/prunus_persica/PRJNA526626_ray/analysis_PE/3_htseq
• calculate tpm
• Load biosamples

[RaymondS1]

PRJNA567655
(69 files)(https://www.ncbi.nlm.nih.gov/Traces/study1/?WebEnv=MCID_5fedeb1cb57f4315fe437f52&query_key=4&GALAXY_URL=https%3A%2F%2Fusegalaxy.org%2Ftool_runner%3Ftool_id%3Dsra_source)

• fastq_dump
  - failed to download SRR10150139 SRR10150140 SRR10150141 SRR10150203 SRR10150207
  - All downloaded
• Run nextflow
  - All 69 completed
  /lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/prunus_persica/PRJNA567655_ray/analysis_PE/3_htseq
• calculate tpm
• Load biosamples