Prunus persica - Expression Analyses

MattHuff commented 4 years ago

BioProject Checklist:

[x] PRJNA526626
[x] PRJNA474565
[x] PRJNA448600
[x] PRJNA439260
[x] PRJNA567655 - Only use the 69 samples from Prunus persica
[x] PRJEB12334
[x] PRJNA454883
[x] PRJNA388577
[x] PRJNA382313
[x] PRJNA353968
[x] PRJNA323761 - Only use the 7 samples from Prunus persica
[x] PRJNA314683
[x] PRJNA268256
[x] PRJNA260463
[x] PRJNA252780
[x] PRJNA248711
[x] PRJNA612533
[x] PRJDB4505

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.

[x] Use the python TPM script to normalize all counts files.
[x] Load all biosamples onto the Hardwoods website.
[ ] Load the normalized counts files onto the Hardwoods website.

patricksis commented 4 years ago

PRJNA474565

[x] fastq_dump (6 SRAs)
[x] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

patricksis commented 4 years ago

PRJNA474565

[x] fastq_dump (6 SRAs)
[x] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

patricksis commented 4 years ago

PRJNA526626

[x] fastq_dump (16 SRAs)
[ ] Run nextflow
[ ] calculate tpm
[ ] Load biosamples Issue with STAR not mapping to genome We're trashing this one, reads are just bad

patricksis commented 4 years ago

PRJNA448600

[x] fastq_dump (8 SRAs)
[x] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

patricksis commented 4 years ago

PRJNA439260

[x] fastq_dump (8 SRAs)
[x] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

patricksis commented 4 years ago

PRJNA567655

[x] fastq_dump (69 SRAs)
[x] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

patricksis commented 4 years ago

PRJNA454883

[x] fastq_dump (32 SRAs)
[x] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

patricksis commented 4 years ago

PRJNA388577

[x] fastq_dump (32 SRAs)
[x] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

patricksis commented 4 years ago

PRJNA382313

[x] fastq_dump (12 SRAs)
[x] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

patricksis commented 4 years ago

PRJNA323761

[x] fastq_dump (7 SRAs)
[x] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

RaymondS1 commented 4 years ago

PRJNA314683

[x] fastq_dump (7 SRAs)
[x] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

RaymondS1 commented 4 years ago

PRJNA268256

[x] fastq_dump (2 SRAs)
- Error prefetch.2.9.0: 'SRR1662174' has no remote vdbcache on prefetch
[ ] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

RaymondS1 commented 4 years ago

PRJNA323761

[x] fastq_dump (7 SRAs)
[x] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

RaymondS1 commented 4 years ago

PRJNA260463

[x] fastq_dump (6 SRAs)
[ ] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

patricksis commented 4 years ago

PRJNA252780

[x] fastq_dump (3 SRAs)
[x] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

patricksis commented 4 years ago

PRJNA248711

[x] fastq_dump (5 SRAs)
[x] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

patricksis commented 4 years ago

PRJNA612533

[x] fastq_dump (73 SRAs)
[x] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

patricksis commented 4 years ago

PRJDB4505

[x] fastq_dump (3 SRAs)
[x] Run nextflow
[ ] calculate tpm
[ ] Load biosamples

patricksis commented 4 years ago

Biosample loader: https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/903619

statonlab / hardwoods_site

Prunus persica - Expression Analyses #575

BioProject Checklist: