Publishing RNA sequencing data analysis scripts on Github before or after Publication?

Question

[m.sadman.sakib]

Hi everyone!

Sorry for this noob question, but I just wanted to ask, what is the best practice in the field for publishing RNA sequencing data analysis scripts? Does it usually happen before the publication, or after? Currently I kept the repo as private and the paper is not published yet.

[GenoMax]

Unless you are doing something super secret making your scripts available should not be a cause of concern.

Answer 1

[jared.andrews07]

Generally, it doesn't really matter unless you're publishing a custom, novel method where the code is really an integral part of the publication. In such a case, you'd want to keep it private until publication. Otherwise, keeping your random DESeq2 scripts in a public repo isn't going to hurt you or draw much attention, though nobody will care if you keep it private until submission either.

Just be sure not to include any PHI or sample information in them.

[m.sadman.sakib]

Thank you very much for the helpful comment!

Answer 2

[Egon Willighagen]

I would strongly recommend publishing them before the paper. That way, you can get your code peer reviewed before you submit your article. That may improve your code. You may have to arrange reviewers yourself for this (maybe an idea for a new BioStars section?).

[m.sadman.sakib]

This will be immensely helpful for others who are learning as well!