Details about submitting the raw RNAseq files to NCBI for my first chapter.

Create an NCBI Account

I logged in through my ORCID account. Started a submission for SRA.

Added the metadata information, project info, etc, according to the NCBI specifications.

SFTP To Transfer files

Followed instructions on NCBI and also got help from Sam (GitHub Issue #2407), and looked at this notebook post of Sam’s.

Used ssh to get into Owl where the data files are. I first copied all the files for this specific project into a new folder so that I could easily transfer them all and not any extra ones.

Owl folder: web/nightingales/P_helianthoides/Grace_Crandall_Chapter1_Files_copy

Then I established an sftp connection:

sftp subftp@sftp-private.ncbi.nlm.nih.gov where subftp is the username. It then prompted me to put in the password given to me by NCBI (will not share).

Then I followed the remaining instructions from NCBI:

  1. navigate to my account folder using: cd uploads/grace[more info that I won't share]
  2. Create a subfolder using: mkdir
  3. Navigate into that newly created subfolder using cd
  4. Copy files into the subfolder using: mput *fastq.gz

Files started transferring around 7:40pm. Completed around 8:33 pm. Takes 10+ minutes for all the files to officially transfer to the folder on the NCBI thing.

“After upload, select your preload folder from the Files step of your submission. Note: it takes at least 10 minutes for uploaded files to become available for selection within a submission.”

Submitted 23:47.

NCBI Info

Will post once official:

SRA: Study: BioProject: BioSample: