Data publication

Data for any paper should be made publically available to support the publication. Common data publication resources include GEO, SRA, Zenodo, etc.

GEO submissions

The Gene Expression Omnibus (GEO) is a genomics data repository. It used to store sequencing-based data such as FASTQs, counts matrices, RDS, etc. Many publication journals require data to be uploaded to GEO or something similar. You’ll need and NCBI account to create a new submission. Follow their instructions and use their metadata sheet template to complete submission. Files can be transfered efficiently using a file transfer protocol (FTP) on the HPC.

Use the module lftp: lftp/4.9.1-GCCcore-8.3.0 (or whatever the latest version is)

module load lftp

## you'll get a password and folder for your submission once you start
lftp ftp-private.ncbi.nlm.nih.gov -u geoftp,<your_password_here>
## if you connect successfully, your prompt will change

cd uploads/your@mail.com_yourfolder
mirror -R Folder_with_submission_files uploads/your@mail.com_yourfolder