When submitting a manuscript to a journal, you are typically required to upload your data (usually fastq files) to an online repository, so that other researchers can download your dataset and replicate your analysis.
SRA (Sequence Read Archive) is one of the largest of these repositories.
https://www.ncbi.nlm.nih.gov/sra
In this guide, we step through the process up uploading your data files that are stored on the HPC to SRA.
Getting started
There is a useful guide and links to uploading your data to SRA here:
https://www.ncbi.nlm.nih.gov/sra/docs/submit/
You should have your sequence data - usually fastq files but can also be bam or other formats - in one directory on the HPC. If they are in a few different directories or in a directory with other data files of the same type (e.g. other fastq files), then create a new directory and copy them to there.
The files should be gzipped. Use the command line gzip tool to create *.gz files, if they are not already gzipped.
Log in to submission portal wizard
The portal wizard will step you through the upload process.
https://submit.ncbi.nlm.nih.gov/subs/sra/
You will need an NCBI account and be logged on with this account to use the wizard. If you don’t have an account, create one now, then log on with that and then click on the above link.
Click