Malus Domestica - Githubissues

statonlab / hardwoods_site

Hardwoods Genomics bugs, data loading, and general issues

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Malus Domestica #606

Open RaymondS1 opened 3 years ago

RaymondS1 commented 3 years ago

BioProject Checklist:

[x] PRJNA493865
[x] PRJNA374502
[x] PRJNA339488
[x] PRJNA306594
[x] PRJDB6779

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

PRJNA493865 Location on the acf /lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/malus_domestica/PRJNA493865_ray 6 SRAs

[x] fastq_dump
[x] Run nextflow
- All completed
[ ] calculate tpm
[ ] Load biosamples

RaymondS1 commented 3 years ago

PRJNA374502 /lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/malus_domestica/PRJNA374502_ray/analysis_SE 12 SRAs

[x] fastq_dump
[x] Run nextflow
- All completed
[ ] calculate tpm
[ ] Load biosamples

RaymondS1 commented 3 years ago

PRJNA339488 /lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/malus_domestica/PRJNA339488_ray 2 SRAs

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

RaymondS1 commented 3 years ago

PRJNA306594 /lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/malus_domestica/PRJNA306594_ray 8 SRAs

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

RaymondS1 commented 3 years ago

PRJDB6779 /lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/malus_domestica/PRJDB6779/analysis 28 SRAs

[x] fastq_dump
[x] Run nextflow
- All completed
[ ] calculate tpm
[ ] Load biosamples