I am using latex for my thesis, using texmaker and mendley for the references. I have used latex and references beforem but I always used Overleaf, so I don't know what I am doing wrong with TexMaker because my refrences appear with a question mark [?] instead of with a number.
This is my code:
% !TEX TS-program = pdflatex
% !TEX encoding = UTF-8 Unicode
% IMPORT SETTINGS
\documentclass[12pt,a4paper,twoside,openright]{report}
\usepackage[justification=centering]{caption}
\input{../include/settings.tex}
% Documents' beginning
\begin{document}
\pagenumbering{roman}
\setcounter{page}{0}
% TITLE PAGE
\input{../include/title_page.tex}
% ENTITIES
\input{../include/empty_page.tex}
\input{../include/entities.tex}
% COPYRIGHT
\input{../include/empty_page.tex}
\input{../include/copyright.tex}
% DEDICATION [OPTIONAL]
% \input{../include/empty_page.tex}
% \input{../include/dedication.tex}
% ACKNOWLEDGMENTS [OPTIONAL]
\input{../include/empty_page.tex}
\input{../include/acknowledgments.tex}
% FINANCING [IF APPLIABLE]
% \input{../include/empty_page.tex}
% \input{../include/financing.tex}
% EPIGRAPH [OPTIONAL]
% \input{../include/empty_page.tex}
% \input{../include/epigraph.tex}
% RESUMO
\input{../include/empty_page.tex}
\input{../abstract/abstract_pt.tex}
% ABSTRACT
\input{../abstract/abstract_en.tex}
%\begin{spacing}{1} % change vertical space between toc, lof, lot and glossaries entries
\printglossaries
\listoffigures
\listoftables
\tableofcontents
%\end{spacing}
% INTRODUCTION
\input{../chapters/introduction/introduction_main.tex}
% METHODS
\input{../chapters/methods/methods_main.tex}
% RESULTS
\input{../chapters/results/results_main.tex}
% CONCLUSION
\input{../chapters/conclusion/conclusion_main.tex}
% REFERENCES / BIBLIOGRAPHY
\cleardoublepage
\bibliography{../references/TESE}
\bibliographystyle{ieeetr}
% INDEX [OPTIONAL]
% Each time you want to add an entry to index you need to use \index{text}
\newpage\null\newpage
\printindex
% APPENDICES [OPTIONAL]
\newpage\null\newpage
\input{../chapters/appendices/appendices_main.tex}
\end{document}
\end{document}
Here is an example of my .bib file called "TESE" generated through Mendeley:
@article{Manganaro2016,
author = {Manganaro, Lorenzo and Attili, Andrea and Dalmasso, Federico and Fausti, Federico and Giordanengo, Simona and Mazza, Giovanni and Monaco, Vincenzo and Sacchi, Roberto and Vignati, Anna and Cirio, Roberto},
journal = {PoS},
keywords = {Intro},
mendeley-tags = {Intro},
title = {{Control of the dose distribution in charged particle therapy}},
url = {http://pos.sissa.it/},
year = {2016}
}
@article{Katiaparodiphysikuni-muenchende2017,
author = {Katiaparodiphysikuni-muenchende, Cc Katia Parodi and Crespo, Paulo},
file = {:D$\backslash$:/Tese/mail{\_}Tese{\_}1.pdf:pdf},
pages = {3--5},
title = {{Master Thesis in M{\"{u}}nchen - Rita Rego}},
year = {2017}
}
Hope someone can help me!

I am sorry if it seems like a "stupid" question but overleaf always did it automatically
– Rita Viegas Nov 14 '17 at 15:58F1to run bibtex and then again two timespdflatex– samcarter_is_at_topanswers.xyz Nov 14 '17 at 16:19