Vitis vinifera - Githubissues

statonlab / hardwoods_site

Hardwoods Genomics bugs, data loading, and general issues

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Vitis vinifera #607

Open RaymondS1 opened 3 years ago

RaymondS1 commented 3 years ago

BioProject Checklist:

[x] PRJNA524691
[x] PRJNA513863
[x] PRJNA488534
[x] PRJNA309491

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

PRJNA524691 Location on the acf /lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/vitis_vinifera/PRJNA524691_ray 4 SRAs

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

RaymondS1 commented 3 years ago

PRJNA513863 110 SRAs

[ ] fastq_dump
- Not completed
[ ] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

RaymondS1 commented 3 years ago

PRJNA488534 /lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/vitis_vinifera/PRJNA488534_ray 36 SRAs

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

RaymondS1 commented 3 years ago

PRJNA309491 /lustre/haven/proj/UTK0032/projects/undergrads/gene_expression_projects/vitis_vinifera/PRJNA309491_ray 3 SRAs

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