Prunus persica - expression analysis

statonlab / hardwoods_site

Hardwoods Genomics bugs, data loading, and general issues

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Prunus persica - expression analysis #605

Open RaymondS1 opened 3 years ago

RaymondS1 commented 3 years ago

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 commented 3 years ago

PRJNA526626 (16 files)

[x] fastq_dump
- failed to download SRR8713333 SRR8713341 SRR8713342 SRR8713343
- All downloaded
[x] 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 commented 3 years ago

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)

[x] fastq_dump
- failed to download SRR10150139 SRR10150140 SRR10150141 SRR10150203 SRR10150207
  - All downloaded
[x] 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