HOWTO: Short Read Archive Submission

  1. Look through the NCBI Short Read Handbook

    • The key part for you to look at is labeled Submission Quick Start Guide
  2. Create an account at

  3. We will need you to fill out the experiment metadata through the NCBI web interface.
  4. We will need you to provide the library IDs for your submission.
  5. With those library IDs we will provide you a list of file names and md5sums for your submission.
  6. We will upload to

SRA/Genome Center phrase book

For us a library lies somewhere between a sample and an experiment, our database doesn't currently track the original sample, only the sample after a certain amount of wet work has been done to it.


Several years ago we submitted RNA-Seq data for our first RNA-Seq paper.


What format should we submit in?
  • The best format for sending data is FASTQ, there are a couple of variants, Phred+33 is prefered.

    See FASTQ format for details about the different versions.

How should the data be processed?
  • The less processing of your FASTQ data the better, the short read archive is storing the "raw" primary data, so we've tried to give them as much of the raw data as possible, and then describe what processing was done in the methods.

Submission/SRA (last edited 2011-01-06 02:03:03 by diane)