SRA uploads to NCBI

This post details the NCBI Sequence Read Archive upload for the sequence data from the Pacuta HI 2022 experiment. The github for that project is here. This protocol is based on A. Huffmyer’s SRA upload post and Putnam Lab SRA upload protocol.

Overview

Below is the following information for this submission.

Sequence Read Archive (SRA) submission: SUB14419354

Submitter

• Jill Ashey; 120 Flagg Road, Kingston RI 02881

General info

• Not associated with current BioProject
• Not associated with current BioSample
• Release date: immediately

Project info

• project title: Pocillopora acuta juvenile RNA-seq
• public description: RNA-seq data from Pocillopora acuta juveniles to future warming and acidification conditions from 2022 Hawaii experiments
• Not associated with umbrella project

Biosample type: invertebrate

Link to submission spreadsheet

Important note so that errors do not occur during upload: After filling out values for attributes provided in the template, your samples are not distinguishable by at least one, or a combination of attributes. Make the combined value of all attributes unique for each sample while taking into account that “sample name”, “sample title” and “description” are not included in this check for “uniqueness”.

SRA metadata

Link to SRA metadata spreadsheet

Files

Upload the fastq.gz files to NCBI with the following code. First, make a new folder that only contains sequence data.

cd /data/putnamlab/jillashey/Pacuta_HI_2022
mkdir raw_file_rnaseq_sra
cd raw_file_rnaseq_sra

ln -s /data/putnamlab/KITT/hputnam/20231127_Scucchia_HI/*fastq.gz .

Use FTP command line file upload to provide files. Activate FTP on the command line. Command prompt now changes to ftp>. Immediately login using the username and password from the NCBI submission portal.

ftp -i
open ftp-private.ncbi.nlm.nih.gov
USERNAME
PASSWORD 

Go into the folder that NCBI provided from the NCBI submission portal. Make a new directory for the files and go into that folder. Put all the sequences from Andromeda into this new folder (they will still be on Andromeda after transfer is complete).

cd uploads/jillashey_uri.edu_XXXXXXXXXXX
mkdir pacuta_2022
cd pacuta_2022
mput *

This takes a few minutes. Once transfers are complete, click select preload folder in the submission portal. Wait until all files have been uploaded and select the pacuta_2022 folder. Click submit!