Open MattHuff opened 4 years ago
Some notes before starting these analyses:
PRJNA268569
PRJNA280092 /staton/software/sratoolkit.2.9.0-centos_linux64/bin/prefetch -v $(<acc_list.txt)
PRJNA380755
PRJNA516042
PRJEB4873
PRJEB17875
PRJNA356360
PRJNA330761
PRJNA325588
PRJEB10691
PRJEB1903
PRJNA354688
I have run the TPM python script on all of the files, and they are ready to be loaded onto the website. If you have biosamples that have not been loaded onto the website, now is the time to do so.
All TPMs have been imported into the site: https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/876994
Re-importing biosamples https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/894657
Publishing biosamples https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/894658
Re-importing expression data https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/894662 following guide https://github.com/mestato/statonlabprivate/wiki/Gene-Expression-Analysis-Lastest-Protocols
Re-importing expression data https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/895347
BioProject Checklist:
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.