Vitis vinifera - expression analysis

MattHuff commented 4 years ago

BioProject Checklist:

[x] PRJNA550508
[x] PRJNA529179
[x] PRJNA528770
[x] PRJNA524691
[x] PRJNA521303
[x] PRJNA516950
[x] PRJNA508364
[x] PRJNA488534
[x] PRJNA476839
[x] PRJNA472397
[x] PRJNA433817
[x] PRJNA418785
[x] PRJNA402079
[x] PRJNA395634
[x] PRJNA390670
[x] PRJNA163649
[x] PRJNA350310
[x] PRJNA348618
[x] PRJNA336064
[x] PRJNA320028
[x] PRJNA312428
[x] PRJNA313234
[x] PRJNA309491
[x] PRJEB30338

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 4 years ago

PRJNA550508

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

RaymondS1 commented 4 years ago

PRJNA529179

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

RaymondS1 commented 4 years ago

PRJNA528770

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

RaymondS1 commented 4 years ago

PRJNA524691

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

RaymondS1 commented 4 years ago

PRJNA521303

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

RaymondS1 commented 4 years ago

PRJNA516950

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

RaymondS1 commented 4 years ago

PRJNA508364

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

RaymondS1 commented 4 years ago

PRJNA488534

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

RaymondS1 commented 4 years ago

PRJNA476839 (both single and paired)

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

RaymondS1 commented 4 years ago

PRJNA472397 (not outputing)

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

RaymondS1 commented 4 years ago

PRJNA433817

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

RaymondS1 commented 4 years ago

PRJNA418785

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

RaymondS1 commented 4 years ago

PRJNA402079

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

RaymondS1 commented 4 years ago

PRJNA395634

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

RaymondS1 commented 4 years ago

PRJNA390670

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

RaymondS1 commented 4 years ago

PRJNA163649

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

RaymondS1 commented 4 years ago

PRJNA350310

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

CaseyRichards92 commented 4 years ago

PRJEB30338

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

RaymondS1 commented 4 years ago

PRJNA348618

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

CaseyRichards92 commented 4 years ago

PRJNA309491

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

CaseyRichards92 commented 4 years ago

Gene Atlas https://hardwoodgenomics.org/Gene-expression-profiling/4244032

CaseyRichards92 commented 4 years ago

PRJNA313234

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

RaymondS1 commented 4 years ago

PRJNA320028

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

RaymondS1 commented 4 years ago

PRJNA312428

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

CaseyRichards92 commented 4 years ago

PRJNA336064

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

statonlab / hardwoods_site

Vitis vinifera - expression analysis #595

BioProject Checklist: