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Where lab outputs go when they become public. Every publication should have code on GitHub, sequencing data in the SRA, and a citable archive where appropriate.

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GitHub

Every publication coming out of the lab has an associated GitHub repo containing the data and code used to create the manuscript figures, so reviewers and readers can reproduce the analyses (example).

• Repos live under the zamanianlab organization.
• All final data, figures, scripts and text associated with a submission should be organized on Box and then transferred to a manuscript-specific repo.
• Account setup and general version control practice are covered in GitHub.

NCBI SRA

Prepare files

1. Ensure proper and informative nomenclature.
2. Compress files with gzip.

Preload the files

1. Navigate to the SRA submission portal and log in or sign up for an NCBI account.
2. Use an SFTP client (e.g. Transmit, CyberDuck) to preload files:
   • On the SRA submit page, click the box that says FTP upload.
   • In your SFTP client, connect to the server using the provided address, username, and password.
   • Navigate to the provided account folder.
   • Make a new folder with a name that describes the submission, such as brugia_tissue_rna.
   • Drag and drop the sequencing files (in FASTQ or BAM format) into the new directory.

Complete the submission wizard

1. Once the preload is complete, click New submission on the SRA wizard home page.

2. Complete the Submitter section and click Continue.

   

   Submitter section

3. Complete the General Info section and click Continue. Unless you are updating previous data, you will probably need to select "No" for both the BioProject and BioSample panes. For "Projected release date," choose the date that you plan to release a pre-print and submit to a journal.

   

   General Info section