Juglans regia - expression analyses

[MattHuff]

BioProject Checklist:

---

• [x] PRJNA335887
• [x] PRJNA319865
• [x] PRJNA272975
• [x] PRJNA235890
• [x] PRJNA237044
• [x] PRJNA232394
• [x] PRJNA613956

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]

Waitin response from ACF due to genome indexing failure error

Jul 09 13:45:28 ..... started STAR run
Jul 09 13:45:28 ... starting to generate Genome files
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted

ppn increased to 8 resolved issue

[CaseyRichards92]

PRJNA335887

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

[CaseyRichards92]

PRJNA319865

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

[CaseyRichards92]

PRJNA272975

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

[CaseyRichards92]

PRJNA235890

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

[CaseyRichards92]

PRJNA237044

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

[CaseyRichards92]

PRJNA232394

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

[CaseyRichards92]

PRJNA613956

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

[CaseyRichards92]

Gene atlas https://hardwoodgenomics.org/Gene-expression-profiling/4210013 Biosample loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/899707 Published Biosamples https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/899711 Expression data loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/899712