In which order should you start writing? In all honesty, if you're motivated to write a particular section, start there and go go go. But, if you aren't sure where to start or are having trouble getting past that blank page, here is the order I recommend:
1) Write methods (you can do this long before you start writing the manuscript, in fact it's much easier if you write a methods section after you revise the protocol after you've performed the experiment a few times)
2) Make figures
3) Write figure legends
4) Storyboard (figure out the best logical flow of the manuscript)
5) Write results. Start by writing each result in point form each result with statistics (or add the stats into a table depending on the type of submission you are planning). Then add the rationale and flow.
6) Write the discussion.
7) Write the introduction
8) Write the abstract
9) Don't forget the title, authors and affiliations, keywords, acknowledgements, author contributions, conflict of interest statement.
10) Check your references. You should have been citing as you have been writing using a citation manager (I recommend you use the one your mentor uses to reduce complications on submission).
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